2RB7

Crystal structure of co-catalytic metallopeptidase (YP_387682.1) from Desulfovibrio desulfuricans G20 at 1.60 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2RB7/pdb

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


• Deposited: 2007-09-18 Released: 2007-10-02 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.180 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 

Literature

Crystal structure of co-catalytic metallopeptidase (YP_387682.1) from Desulfovibrio desulfuricans G20 at 1.60 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 81.73 kDa 
• Atom Count: 6,754 
• Modelled Residue Count: 720 
• Deposited Residue Count: 728 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase, M20/M25/M40 family	A, B	364	Oleidesulfovibrio alaskensis G20	Mutation(s): 0  Gene Names: YP_387682.1, Dde_1186 EC: 3.5.1.18
UniProt
Find proteins for Q313A9 (Oleidesulfovibrio alaskensis (strain ATCC BAA-1058 / DSM 17464 / G20)) Explore Q313A9  Go to UniProtKB:  Q313A9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	E [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	C [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	D [auth A], F [auth B], G [auth B], H [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-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: 1.60 Å
• R-Value Free: 0.180 
• R-Value Work: 0.154 
• R-Value Observed: 0.155 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M32RB7

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.85	α = 90
b = 82.19	β = 91.37
c = 89.34	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-02 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-10-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-01-25
  Changes: Database references
• Version 1.5: 2024-10-30
  Changes: Data collection, Structure summary