3HM4 | pdb_00003hm4

CRYSTAL STRUCTURE OF A CHEMOTAXIS PROTEIN CHEX (DDE_0281) FROM DESULFOVIBRIO DESULFURICANS SUBSP. AT 1.30 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3HM4/pdb

• Classification: HYDROLASE
• Organism(s): Oleidesulfovibrio alaskensis G20
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-05-28 Released: 2009-06-23 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.165 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Literature

Crystal structure of Chemotaxis protein CheX (YP_386777.1) from DESULFOVIBRIO DESULFURICANS G20 at 1.30 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: 33.22 kDa 
• Atom Count: 2,633 
• Modeled Residue Count: 303 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chemotaxis protein CheX	A, B	156	Oleidesulfovibrio alaskensis G20	Mutation(s): 0  Gene Names: Dde_0281, YP_386777.1
UniProt
Find proteins for Q316R4 (Oleidesulfovibrio alaskensis (strain ATCC BAA-1058 / DSM 17464 / G20)) Explore Q316R4  Go to UniProtKB:  Q316R4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
UNL	C [auth A]	Unknown ligand PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33HM4

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.362	α = 90
b = 73.999	β = 90
c = 83.338	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-23 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-06-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, 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: 2024-11-27
  Changes: Data collection, Structure summary