3KHN

Crystal structure of putative MotB like protein DVU_2228 from Desulfovibrio vulgaris.

• PDB DOI: https://doi.org/10.2210/pdb3KHN/pdb

• Classification: structural genomics, unknown function
• Organism(s): Nitratidesulfovibrio vulgaris str. Hildenborough
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-10-30 Released: 2009-12-01 
• Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.251 
• R-Value Work: 0.185 
• R-Value Observed: 0.189 

Literature

Crystal structure of putative MotB like protein DVU_2228 from Desulfovibrio vulgaris

Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C.

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: 39.79 kDa 
• Atom Count: 2,719 
• Modelled Residue Count: 319 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MotB protein, putative	A, B	174	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0  Gene Names: DVU_2228
UniProt
Find proteins for Q729W9 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q729W9  Go to UniProtKB:  Q729W9

Small Molecules

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: 2.03 Å
• R-Value Free: 0.251 
• R-Value Work: 0.185 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.218	α = 90
b = 83.709	β = 90
c = 85.891	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHELXE	model building
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-01 
Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Structure summary