2O34

Crystal structure of protein DVU1097 from Desulfovibrio vulgaris Hildenborough, Pfam DUF375

• PDB DOI: https://doi.org/10.2210/pdb2O34/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Nitratidesulfovibrio vulgaris
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-11-30 Released: 2006-12-12 
• Deposition Author(s): Malashkevich, V.N., Toro, R., Sauder, J.M., Schwinn, K.D., Thompson, D.A., Rutter, M.E., Dickey, M., Groshong, C., Bain, K.T., Adams, J.M., Reyes, C., Rooney, I., Powell, A., Boice, A., Gheyi, T., Ozyurt, S., Atwell, S., Wasserman, S.R., Emtage, S., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.273 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Crystal Structure of the Hypothetical Protein from Desulfovibrio vulgaris Hildenborough

Malashkevich, V.N., Toro, R., Sauder, J.M., Thompson, D.A., Rutter, M.E., Dickey, M., Groshong, C., Bain, K.T., Adams, J.M., Reyes, C., Rooney, I., Powell, A., Boice, A., Gheyi, T., Ozyurt, S., Atwell, S., Wasserman, S.R., Schwinn, K.D., Emtage, S., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 53.91 kDa 
• Atom Count: 3,943 
• Modelled Residue Count: 480 
• Deposited Residue Count: 500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B	250	Nitratidesulfovibrio vulgaris	Mutation(s): 8
UniProt
Find proteins for Q72D34 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72D34  Go to UniProtKB:  Q72D34

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A], D [auth A], E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-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: 1.95 Å
• R-Value Free:  0.273 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.48	α = 90
b = 81.48	β = 90
c = 151.17	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SHELX	refinement
DENZO	data reduction
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-12 
Deposition Author(s): Malashkevich, V.N., Toro, R., Sauder, J.M., Schwinn, K.D., Thompson, D.A., Rutter, M.E., Dickey, M., Groshong, C., Bain, K.T., Adams, J.M., Reyes, C., Rooney, I., Powell, A., Boice, A., Gheyi, T., Ozyurt, S., Atwell, S., Wasserman, S.R., Emtage, S., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2006-12-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.5: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.6: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.7: 2023-12-27
  Changes: Data collection, Database references
• Version 1.8: 2024-11-06
  Changes: Structure summary