3KD8

Cofactor-Independent Phosphoglycerate mutase from Thermoplasma Acidophilum DSM 1728

PDB DOI: https://doi.org/10.2210/pdb3KD8/pdb

Classification: ISOMERASE
Organism(s): Thermoplasma acidophilum
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2009-10-22 Released: 2009-12-01
Deposition Author(s): Joachimiak, A., Duke, N.E.C., Marshall, N., Buck, K., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.288
R-Value Work: 0.207
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

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

Literature

Cofactor-Independent Phosphoglycerate mutase from Thermoplasma Acidophilum DSM 1728

Joachimiak, A., Duke, N.E.C., Marshall, N., Buck, K.

To be published.

Macromolecule Content

Total Structure Weight: 87.93 kDa
Atom Count: 5,761
Modelled Residue Count: 732
Deposited Residue Count: 798
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,3-bisphosphoglycerate-independent phosphoglycerate mutase	A, B	399	Thermoplasma acidophilum	Mutation(s): 0 Gene Names: apgM, Ta0413 EC: 5.4.2.1
UniProt
Find proteins for Q9HL27 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HL27 Go to UniProtKB: Q9HL27
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HL27
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.288
R-Value Work: 0.207
R-Value Observed: 0.211
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.911	α = 90
b = 137.081	β = 90
c = 67.088	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-12-01

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-12-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance

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.