3IDD | pdb_00003idd

Cofactor-Independent Phosphoglycerate Mutase from Thermoplasma acidophilum DSM 1728

PDB DOI: https://doi.org/10.2210/pdb3IDD/pdb

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

Deposited: 2009-07-20 Released: 2009-10-06
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: 2.80 Å
R-Value Free:
0.311 (Depositor), 0.233 (DCC)
R-Value Work:
0.230 (Depositor), 0.235 (DCC)
R-Value Observed:
0.234 (Depositor)

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This is version 1.2 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: 89.84 kDa
Atom Count: 5,667
Modeled Residue Count: 725
Deposited Residue Count: 814
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,3-bisphosphoglycerate-independent phosphoglycerate mutase	A, B	407	Thermoplasma acidophilum	Mutation(s): 0 Gene Names: apgM, Ta0413 EC: 5.4.2.1 (PDB Primary Data), 5.4.2.12 (UniProt)
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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: 2.80 Å
R-Value Free: 0.311 (Depositor), 0.233 (DCC)
R-Value Work: 0.230 (Depositor), 0.235 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.605	α = 90
b = 136.744	β = 90
c = 63.289	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

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Entry History

Deposition Data

Released Date: 2009-10-06

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-10-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.