1U55: Crystal Structure Of An Oxygen Binding H-NOX Domain Related ...

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229,380 Structures from the PDB 1,068,577 Computed Structure Models (CSM)

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Data API 1U55

Crystal structure of an oxygen binding H-NOX domain related to soluble guanylate cyclases (oxygen complex)

• PDB DOI: https://doi.org/10.2210/pdb1U55/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Caldanaerobacter subterraneus subsp. tengcongensis
• Expression System: Escherichia coli
• Mutation(s): No 
• Deposited: 2004-07-27 Released: 2004-08-31 
• Deposition Author(s): Pellicena, P., Karow, D.S., Boon, E.M., Marletta, M.A., Kuriyan, J.

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.257 
• R-Value Work: 0.227 

Starting Model: experimentalView more details

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history. LiteratureDownload Primary Citation 

•  Download Mendeley

Crystal structure of an oxygen-binding heme domain related to soluble guanylate cyclases.

Pellicena, P., Karow, D.S., Boon, E.M., Marletta, M.A., Kuriyan, J.

(2004) Proc Natl Acad Sci U S A 101: 12854-12859

• PubMed: 15326296 Search on PubMedSearch on PubMed Central
• DOI: https://doi.org/10.1073/pnas.0405188101
• Primary Citation of Related Structures:  1U4H, 1U55, 1U56
• PubMed Abstract: 

  Soluble guanylate cyclases are nitric oxide-responsive signaling proteins in which the nitric oxide sensor is a heme-binding domain of unknown structure that we have termed the heme-NO and oxygen binding (H-NOX) domain. H-NOX domains are also found in bacteria, either as isolated domains, or are fused through a membrane-spanning region to methyl-accepting chemotaxis proteins. We have determined the crystal structure of an oxygen-binding H-NOX domain of one such signaling protein from the obligate anaerobe Thermoanaerobacter tengcongensis at 1.77-angstroms resolution, revealing a protein fold unrelated to known structures. Particularly striking is the structure of the protoporphyrin IX group, which is distorted from planarity to an extent not seen before in protein-bound heme groups. Comparison of the structure of the H-NOX domain in two different crystal forms suggests a mechanism whereby alteration in the degree of distortion of the heme group is coupled to changes on the molecular surface of the H-NOX domain and potentially to changes in intermolecular interactions.

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Organizational Affiliation: 

Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.

Asymmetric Unit

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

Biological Assembly 1  

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

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 (HEM)

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

Biological assembly 2 assigned by authors.

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Macromolecule Content

• Total Structure Weight: 45.43 kDa 
• Atom Count: 3,440 
• Modelled Residue Count: 375 
• Deposited Residue Count: 376 
• Unique protein chains: 1

MacromoleculesFind similar proteins by: Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heme-based Methyl-accepting Chemotaxis Protein	A, B	188	Caldanaerobacter subterraneus subsp. tengcongensis	Mutation(s): 0 Gene Names: Tar4
UniProt
Find proteins for Q8RBX6 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4))Explore Q8RBX6 Go to UniProtKB:  Q8RBX6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8RBX6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEMQuery on HEMDownload Ideal Coordinates CCD File Download Instance Coordinates SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A],F [auth B]	PROTOPORPHYRIN IX CONTAINING FEC34 H32 Fe N4 O4KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
CLQuery on CLDownload Ideal Coordinates CCD File Download Instance Coordinates SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	CHLORIDE IONClVEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
OXYQuery on OXYDownload Ideal Coordinates CCD File Download Instance Coordinates SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A],G [auth B]	OXYGEN MOLECULEO2MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 0.257 
• R-Value Work: 0.227 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.48	α = 90
b = 126.99	β = 94.33
c = 42.572	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

View more in-depth experimental dataEntry History 

Deposition Data

• Released Date: 2004-08-31 
Deposition Author(s): Pellicena, P., Karow, D.S., Boon, E.M., Marletta, M.A., Kuriyan, J.

Revision History (Full details and data files)

• Version 1.0: 2004-08-31Type: Initial release
• Version 1.1: 2008-04-30Changes: Version format compliance
• Version 1.2: 2011-07-13Changes: Version format compliance
• Version 1.3: 2023-08-23Changes: Data collection, Database references, Derived calculations, Refinement description

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