4FCE | pdb_00004fce

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

• PDB DOI: https://doi.org/10.2210/pdb4FCE/pdb

• Classification: TRANSFERASE
• Organism(s): Yersinia pestis CO92
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-24 Released: 2012-07-11 
• Deposition Author(s): Nocek, B., Kuhn, M., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 49.67 kDa 
• Atom Count: 3,660 
• Modeled Residue Count: 441 
• Deposited Residue Count: 459 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional protein GlmU	A	459	Yersinia pestis CO92	Mutation(s): 0  Gene Names: glmU, YPTB3965 EC: 2.7.7.23 (PDB Primary Data), 2.3.1.157 (PDB Primary Data)
UniProt
Find proteins for Q8Z9S7 (Yersinia pestis) Explore Q8Z9S7  Go to UniProtKB:  Q8Z9S7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GP1	D [auth A]	2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose C6 H14 N O8 P YMJBYRVFGYXULK-QZABAPFNSA-N
EDO	E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34fce

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.571	α = 90
b = 87.571	β = 90
c = 251.368	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-11 
Deposition Author(s): Nocek, B., Kuhn, M., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• 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
• Version 2.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary