2P2U | pdb_00002p2u

Crystal structure of putative host-nuclease inhibitor protein Gam from Desulfovibrio vulgaris

• PDB DOI: https://doi.org/10.2210/pdb2P2U/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Nitratidesulfovibrio vulgaris
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-03-07 Released: 2007-03-27 
• Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Zhang, F., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.290 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Literature

Crystal structure of putative host-nuclease inhibitor protein Gam from Desulfovibrio vulgaris

Bonanno, J.B., Rutter, M., Bain, K.T., Zhang, F., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., 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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 38.96 kDa 
• Atom Count: 2,424 
• Modeled Residue Count: 303 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Host-nuclease inhibitor protein Gam, putative	A, B	171	Nitratidesulfovibrio vulgaris	Mutation(s): 6  Gene Names: DVU_1136
UniProt
Find proteins for Q72CZ5 (Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore Q72CZ5  Go to UniProtKB:  Q72CZ5

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: 2.75 Å
• R-Value Free:  0.290 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.03	α = 90
b = 93.408	β = 90
c = 104.166	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-27 
Deposition Author(s): Bonanno, J.B., Rutter, M., Bain, K.T., Zhang, F., Romero, R., Smith, D., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-03-27
  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: 2012-10-24
  Changes: Structure summary
• Version 1.4: 2017-10-18
  Changes: Refinement description
• Version 1.5: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.6: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.7: 2024-10-16
  Changes: Data collection, Database references, Structure summary