2Q04

Crystal structure of acetoin utilization protein (ZP_00540088.1) from Exiguobacterium sibiricum 255-15 at 2.33 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Crystal structure of acetoin utilization protein (ZP_00540088.1) from Exiguobacterium sibiricum 255-15 at 2.33 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acetoin utilization protein
A, B, C, D, E, F
211Exiguobacterium sibiricum 255-15Mutation(s): 8 
Gene Names: ZP_00540088.1ExigDRAFT_0571Exig_2238
Find proteins for B1YKD7 (Exiguobacterium sibiricum (strain DSM 17290 / JCM 13490 / 255-15))
Go to UniProtKB:  B1YKD7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download CCD File 
A, C, D, F
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

Download CCD File 
A, E, F
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B, C, D, E, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A,B,C,D,E,F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 1 21 1
  • Diffraction Data DOI: 2Q04 Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.87α = 90
b = 128.58β = 108.43
c = 108.43γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
autoSHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-12
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2017-10-25
    Changes: Author supporting evidence
  • Version 1.5: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description