3JR7 | pdb_00003jr7

The crystal structure of the protein of DegV family COG1307 with unknown function from Ruminococcus gnavus ATCC 29149

• PDB DOI: https://doi.org/10.2210/pdb3JR7/pdb

• Classification: structural genomics, unknown function
• Organism(s): Mediterraneibacter gnavus ATCC 29149
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-09-08 Released: 2009-10-20 
• Deposition Author(s): Zhang, R., Hatzos, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.208 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 5V85

Literature

The crystal structure of the protein of DegV family COG1307 with unknown function from Ruminococcus gnavus ATCC 29149

Zhang, R., Hatzos, C., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 68.08 kDa 
• Atom Count: 4,889 
• Modeled Residue Count: 558 
• Deposited Residue Count: 596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized egV family protein COG1307	A, B	298	Mediterraneibacter gnavus ATCC 29149	Mutation(s): 0  Gene Names: RUMGNA_03254
UniProt
Find proteins for A7B6P0 (Mediterraneibacter gnavus (strain ATCC 29149 / DSM 114966 / JCM 6515 / VPI C7-9)) Explore A7B6P0  Go to UniProtKB:  A7B6P0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG6	C [auth A], H [auth B]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C12 H26 O6 DMDPGPKXQDIQQG-UHFFFAOYSA-N
PO4	D [auth A], I [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA	E [auth A], F [auth A], G [auth A], J [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: 2.00 Å
• R-Value Free:  0.208 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.899	α = 90
b = 96.899	β = 90
c = 159.921	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-20 
Deposition Author(s): Zhang, R., Hatzos, C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary