5VVE | pdb_00005vve

Crystal structure of phosphoglycerate mutase from Naegleria fowleri

PDB DOI: https://doi.org/10.2210/pdb5VVE/pdb

Classification: ISOMERASE
Organism(s): Naegleria fowleri
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-05-19 Released: 2017-08-30
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.195 (Depositor), 0.187 (DCC)
R-Value Work:
0.165 (Depositor)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5VVE

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of phosphoglycerate mutase from Naegleria fowleri

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

To be published.

Macromolecule Content

Total Structure Weight: 60.48 kDa
Atom Count: 4,725
Modeled Residue Count: 489
Deposited Residue Count: 516
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate mutase	A, B	258	Naegleria fowleri	Mutation(s): 0 Gene Names: NF0048460 EC: 5.4.2.11
UniProt
Find proteins for A0A2D0TCG6 (Naegleria fowleri) Explore A0A2D0TCG6 Go to UniProtKB: A0A2D0TCG6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2D0TCG6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B]	E [auth A], F [auth A], H [auth B], I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.195 (Depositor), 0.187 (DCC)
R-Value Work: 0.165 (Depositor)
R-Value Observed: 0.166 (Depositor)

Diffraction Data:

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.61	α = 90
b = 89.33	β = 90
c = 157.88	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-08-30

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-08-30
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.