5UM0 | pdb_00005um0

Crystal structure of 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase from Neisseria gonorrhoeae

• PDB DOI: https://doi.org/10.2210/pdb5UM0/pdb

• Classification: ISOMERASE
• Organism(s): Neisseria gonorrhoeae NCCP11945
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-01-25 Released: 2017-02-15 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase from Neisseria gonorrhoeae

Abendroth, J., Lorimer, D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 108.59 kDa 
• Atom Count: 8,393 
• Modeled Residue Count: 918 
• Deposited Residue Count: 940 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase	A, B, C, D	235	Neisseria gonorrhoeae NCCP11945	Mutation(s): 0  Gene Names: gpmA, NGK_0248 EC: 5.4.2.11
UniProt
Find proteins for B4RIY7 (Neisseria gonorrhoeae (strain NCCP11945)) Explore B4RIY7  Go to UniProtKB:  B4RIY7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	E [auth A], F [auth B], G [auth C], H [auth D]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35UM0

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.58	α = 90
b = 73.03	β = 97.6
c = 96.93	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-15 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2017-02-15
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description