3KD8 | pdb_00003kd8

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.288 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Cofactor-Independent Phosphoglycerate mutase from Thermoplasma Acidophilum DSM 1728

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

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

Macromolecules

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 (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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

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

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2009-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary