3H4Y | pdb_00003h4y

Crystal structure of putative chemotaxis protein (YP_009526.1) from DESULFOVIBRIO VULGARIS HILDENBOROUGH at 1.55 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3H4Y/pdb

• Classification: HYDROLASE
• Organism(s): Nitratidesulfovibrio vulgaris str. Hildenborough
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-21 Released: 2009-05-05 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.196 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Literature

Crystal structure of putative chemotaxis protein (YP_009526.1) from DESULFOVIBRIO VULGARIS HILDENBOROUGH at 1.55 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.95 kDa 
• Atom Count: 1,327 
• Modeled Residue Count: 154 
• Deposited Residue Count: 156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative chemotaxis protein	A	156	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0  Gene Names: DVU_0302, YP_009526.1
UniProt
Find proteins for Q72FB2 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72FB2  Go to UniProtKB:  Q72FB2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	B [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
MRD	C [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.196 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33H4Y

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.82	α = 90
b = 43.82	β = 90
c = 158.604	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-05 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-16
  Changes: Data collection, Structure summary