4QG5 | pdb_00004qg5

Crystal structure of phosphoglucomutase from Leishmania major at 3.5 angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb4QG5/pdb

Classification: ISOMERASE
Organism(s): Leishmania major
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-05-22 Released: 2015-05-27
Deposition Author(s): Waugh, B., Sen, U., Banerjee, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.315 (Depositor), 0.317 (DCC)
R-Value Work:
0.238 (Depositor), 0.245 (DCC)
R-Value Observed:
0.242 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of phosphoglucomutase from Leishmania major at 3.5 angstrom resolution

Waugh, B., Sen, U., Banerjee, R.

To be published.

Macromolecule Content

Total Structure Weight: 257.08 kDa
Atom Count: 17,136
Modeled Residue Count: 2,244
Deposited Residue Count: 2,368
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative phosphoglucomutase	A, B, C, D	592	Leishmania major	Mutation(s): 0 Gene Names: LMJF_21_0640 EC: 5.4.2.2
UniProt
Find proteins for Q4QCF1 (Leishmania major) Explore Q4QCF1 Go to UniProtKB: Q4QCF1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4QCF1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-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: 3.50 Å
R-Value Free: 0.315 (Depositor), 0.317 (DCC)
R-Value Work: 0.238 (Depositor), 0.245 (DCC)
R-Value Observed: 0.242 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 202.358	α = 90
b = 114.971	β = 110.03
c = 125.915	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-05-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-05-27
Type: Initial release
Version 1.1: 2016-04-20
Changes: Experimental preparation
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, 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.