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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.209 (Depositor), 0.213 (DCC)
R-Value Work:
0.166 (Depositor), 0.169 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

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

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

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B4RIY7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TLA Query on TLA Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.209 (Depositor), 0.213 (DCC)
R-Value Work: 0.166 (Depositor), 0.169 (DCC)
R-Value Observed: 0.167 (Depositor)

Diffraction Data:

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

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Entry History

Deposition Data

Released Date: 2017-02-15

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.