3CT9

Crystal structure of a putative zinc peptidase (NP_812461.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.31 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of a Putative Zinc Peptidase (NP_812461.1) from Bacteroides thetaiotaomicron VPI-5482 at 2.31 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Acetylornithine deacetylaseA, B356Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
Gene Names: NP_812461.1BT_3549
Find proteins for Q8A1V9 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482))
Explore Q8A1V9 
Go to UniProtKB:  Q8A1V9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
V [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], S [auth B], T [auth B], U [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], H [auth A], P [auth B], Q [auth B], R [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.34α = 90
b = 67.25β = 94.28
c = 107.89γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SOLVEphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-05-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, 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