3GSE

Crystal structure of menaquinone-specific isochorismate synthase from Yersinia pestis CO92

• PDB DOI: https://doi.org/10.2210/pdb3GSE/pdb

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


• Deposited: 2009-03-26 Released: 2009-05-05 
• Deposition Author(s): Nocek, B., Gu, M., Papazisi, L., 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: 2.28 Å
• R-Value Free: 0.252 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 

Starting Model: experimental

Literature

Crystal structure of menaquinone-specific isochorismate synthase from Yersinia pestis CO92

Nocek, B., Gu, M., Papazisi, L., Anderson, W.F., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 51.61 kDa 
• Atom Count: 3,549 
• Modelled Residue Count: 425 
• Deposited Residue Count: 458 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Menaquinone-specific isochorismate synthase	A	458	Yersinia pestis	Mutation(s): 0  Gene Names: menF, YPO2528 EC: 5.4.4.2
UniProt
Find proteins for Q8D0S5 (Yersinia pestis) Explore Q8D0S5  Go to UniProtKB:  Q8D0S5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.252 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/m33gse

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.19	α = 90
b = 76.997	β = 90.39
c = 70.414	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-05 
Deposition Author(s): Nocek, B., Gu, M., Papazisi, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2009-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description