2PYJ: Phi29 DNA Polymerase Complexed With Primer ... - RCSB PDB

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246,715Structures from the PDB archive 1,068,577Computed Structure Models (CSM)

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Data API 2PYJ | pdb_00002pyj

Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex)

• PDB DOI: https://doi.org/10.2210/pdb2PYJ/pdb
• NAKB: 2PYJ

• Classification: REPLICATION, TRANSFERASE/DNA
• Organism(s): Salasvirus phi29
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Deposited: 2007-05-16 Released: 2007-07-17 
• Deposition Author(s): Berman, A.J., Kamtekar, S., Goodman, J.L., Lazaro, J.M., de Vega, M., Blanco, L., Salas, M., Steitz, T.A.

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free:  0.234 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Starting Model: experimentalView more details

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.5 of the entry. See complete history. LiteratureDownload Primary Citation 

•  Download Mendeley

Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases

Berman, A.J., Kamtekar, S., Goodman, J.L., Lazaro, J.M., de Vega, M., Blanco, L., Salas, M., Steitz, T.A.

(2007) EMBO J 26: 3494-3505

• PubMed: 17611604 Search on PubMedSearch on PubMed Central
• DOI: https://doi.org/10.1038/sj.emboj.7601780
• Primary Citation of Related Structures:  2PY5, 2PYJ, 2PYL, 2PZS
• PubMed Abstract: 

  Replicative DNA polymerases (DNAPs) move along template DNA in a processive manner. The structural basis of the mechanism of translocation has been better studied in the A-family of polymerases than in the B-family of replicative polymerases. To address this issue, we have determined the X-ray crystal structures of phi29 DNAP, a member of the protein-primed subgroup of the B-family of polymerases, complexed with primer-template DNA in the presence or absence of the incoming nucleoside triphosphate, the pre- and post-translocated states, respectively. Comparison of these structures reveals a mechanism of translocation that appears to be facilitated by the coordinated movement of two conserved tyrosine residues into the insertion site. This differs from the mechanism employed by the A-family polymerases, in which a conserved tyrosine moves into the templating and insertion sites during the translocation step. Polymerases from the two families also interact with downstream single-stranded template DNA in very different ways.

   View More
Organizational Affiliation: 
• Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

Asymmetric Unit

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (DGT)

Biological Assembly 1  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (DGT)

Global Symmetry: Asymmetric - C1 Global Stoichiometry: Monomer - A1 LessFind Similar Assemblies

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (DGT)

Global Symmetry: Asymmetric - C1 Global Stoichiometry: Monomer - A1 LessFind Similar Assemblies

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (DGT)

Find Similar Assemblies

Biological assembly 3 assigned by authors.

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Macromolecule Content 

• Total Structure Weight: 158.99 kDa 
• Atom Count: 11,997 
• Modeled Residue Count: 1,210 
• Deposited Residue Count: 1,222 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

MacromoleculesProteins 1Nucleic Acids / Hybrid 2Find similar proteins by: Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	G [auth A],H [auth B]	575	Salasvirus phi29	Mutation(s): 2 Gene Names: 2, gp2EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
UniProt
Find proteins for P03680 (Bacillus phage phi29)Explore P03680 Go to UniProtKB:  P03680
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03680
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-d(GACTGCTTA(DOC)-3'	A [auth X],C [auth Q],F [auth J]	10	N/A
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-d(ACACGTAAGCAGTC)-3'	B [auth Y],D [auth R],E [auth K]	14	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DGTQuery on DGTDownload Ideal Coordinates CCD File Download Instance Coordinates SDF format, chain NA [auth B] SDF format, chain T [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain T [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain T [auth A]	NA [auth B],T [auth A]	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATEC10 H16 N5 O13 P3HAAZLUGHYHWQIW-KVQBGUIXSA-N		Interactions Focus chain NA [auth B] Focus chain T [auth A] Interactions & Density Focus chain NA [auth B] Focus chain T [auth A]
EDOQuery on EDODownload Ideal Coordinates CCD File Download Instance Coordinates SDF format, chain AA [auth A] SDF format, chain AB [auth B] SDF format, chain BA [auth A] SDF format, chain BB [auth B] SDF format, chain CA [auth A] SDF format, chain CB [auth B] SDF format, chain DA [auth A] SDF format, chain EA [auth A] SDF format, chain FA [auth A] SDF format, chain GA [auth A] SDF format, chain HA [auth A] SDF format, chain I [auth X] SDF format, chain IA [auth A] SDF format, chain J [auth X] SDF format, chain JA [auth A] SDF format, chain K [auth Y] SDF format, chain KA [auth A] SDF format, chain L [auth Y] SDF format, chain M [auth Q] SDF format, chain N [auth R] SDF format, chain O [auth K] SDF format, chain OA [auth B] SDF format, chain P [auth K] SDF format, chain PA [auth B] SDF format, chain Q [auth K] SDF format, chain QA [auth B] SDF format, chain RA [auth B] SDF format, chain SA [auth B] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain Z [auth A] SDF format, chain ZA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain CB [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain I [auth X] MOL2 format, chain IA [auth A] MOL2 format, chain J [auth X] MOL2 format, chain JA [auth A] MOL2 format, chain K [auth Y] MOL2 format, chain KA [auth A] MOL2 format, chain L [auth Y] MOL2 format, chain M [auth Q] MOL2 format, chain N [auth R] MOL2 format, chain O [auth K] MOL2 format, chain OA [auth B] MOL2 format, chain P [auth K] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth K] MOL2 format, chain QA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain BB [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain CB [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain I [auth X] mmCIF format, chain IA [auth A] mmCIF format, chain J [auth X] mmCIF format, chain JA [auth A] mmCIF format, chain K [auth Y] mmCIF format, chain KA [auth A] mmCIF format, chain L [auth Y] mmCIF format, chain M [auth Q] mmCIF format, chain N [auth R] mmCIF format, chain O [auth K] mmCIF format, chain OA [auth B] mmCIF format, chain P [auth K] mmCIF format, chain PA [auth B] mmCIF format, chain Q [auth K] mmCIF format, chain QA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth B]	AA [auth A]AB [auth B]BA [auth A]BB [auth B]CA [auth A]AA [auth A],AB [auth B],BA [auth A],BB [auth B],CA [auth A],CB [auth B],DA [auth A],EA [auth A],FA [auth A],GA [auth A],HA [auth A],I [auth X],IA [auth A],J [auth X],JA [auth A],K [auth Y],KA [auth A],L [auth Y],M [auth Q],N [auth R],O [auth K],OA [auth B],P [auth K],PA [auth B],Q [auth K],QA [auth B],RA [auth B],SA [auth B],TA [auth B],U [auth A],UA [auth B],V [auth A],VA [auth B],W [auth A],WA [auth B],X [auth A],XA [auth B],Y [auth A],YA [auth B],Z [auth A],ZA [auth B] Less	1,2-ETHANEDIOLC2 H6 O2LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain I [auth X] Focus chain IA [auth A] Focus chain J [auth X] Focus chain JA [auth A] Focus chain K [auth Y] Focus chain KA [auth A] Focus chain L [auth Y] Focus chain M [auth Q] Focus chain N [auth R] Focus chain O [auth K] Focus chain OA [auth B] Focus chain P [auth K] Focus chain PA [auth B] Focus chain Q [auth K] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CA [auth A] Focus chain CB [auth B] Focus chain DA [auth A] Focus chain EA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain HA [auth A] Focus chain I [auth X] Focus chain IA [auth A] Focus chain J [auth X] Focus chain JA [auth A] Focus chain K [auth Y] Focus chain KA [auth A] Focus chain L [auth Y] Focus chain M [auth Q] Focus chain N [auth R] Focus chain O [auth K] Focus chain OA [auth B] Focus chain P [auth K] Focus chain PA [auth B] Focus chain Q [auth K] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B]
MNQuery on MNDownload Ideal Coordinates CCD File Download Instance Coordinates SDF format, chain LA [auth B] SDF format, chain R [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain R [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain R [auth A]	LA [auth B],R [auth A]	MANGANESE (II) IONMnWAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain LA [auth B] Focus chain R [auth A] Interactions & Density Focus chain LA [auth B] Focus chain R [auth A]
MGQuery on MGDownload Ideal Coordinates CCD File Download Instance Coordinates SDF format, chain MA [auth B] SDF format, chain S [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain S [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain S [auth A]	MA [auth B],S [auth A]	MAGNESIUM IONMgJLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain MA [auth B] Focus chain S [auth A] Interactions & Density Focus chain MA [auth B] Focus chain S [auth A]

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free:  0.234 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1 21 1Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.835	α = 90
b = 114.667	β = 94.07
c = 104.761	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

View more in-depth experimental dataEntry History 

Deposition Data

• Released Date: 2007-07-17 
Deposition Author(s): Berman, A.J., Kamtekar, S., Goodman, J.L., Lazaro, J.M., de Vega, M., Blanco, L., Salas, M., Steitz, T.A.

Revision History (Full details and data files)

• Version 1.0: 2007-07-17Type: Initial release
• Version 1.1: 2008-05-01Changes: Version format compliance
• Version 1.2: 2011-07-13Changes: Version format compliance
• Version 1.3: 2020-04-15Changes: Data collection, Derived calculations
• Version 1.4: 2021-10-20Changes: Database references, Derived calculations
• Version 1.5: 2023-08-30Changes: Data collection, Refinement description

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