4FCE

Crystal structure of Yersinia pestis GlmU in complex with alpha-D-glucosamine 1-phosphate (GP1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal structure of Yersinia pestis GlmU in complex with alpha-D-glucosamine 1-phosphate (GP1)

Nocek, B.Kuhn, M.Anderson, W.F.Joachimiak, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bifunctional protein GlmU A459Yersinia pestis CO92Mutation(s): 0 
Gene Names: glmUYPTB3965
EC: 2.7.7.23 (PDB Primary Data), 2.3.1.157 (PDB Primary Data)
Find proteins for Q8Z9S7 (Yersinia pestis)
Explore Q8Z9S7 
Go to UniProtKB:  Q8Z9S7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GP1
Query on GP1

Download Ideal Coordinates CCD File 
A
2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose
C6 H14 N O8 P
YMJBYRVFGYXULK-QZABAPFNSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.571α = 90
b = 87.571β = 90
c = 251.368γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing
REFMACrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-11
    Type: Initial release
  • Version 1.1: 2015-10-21
    Changes: Source and taxonomy
  • Version 1.2: 2016-09-28
    Changes: Structure summary
  • Version 1.3: 2016-12-14
    Changes: Structure summary
  • Version 1.4: 2017-11-15
    Changes: Refinement description
  • Version 1.5: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary