3KKK | pdb_00003kkk

Y92C catalytic residue mutant of Phosphoglycerate Mutase from Plasmodium falciparum

• PDB DOI: https://doi.org/10.2210/pdb3KKK/pdb

• Classification: ISOMERASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-11-05 Released: 2009-11-17 
• Deposition Author(s): Larson, E.T., Merritt, E.A., Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.236 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structure of a phosphoglycerate mutase from Plasmodium falciparum

Larson, E.T., Caruthers, J.M., Zhang, L., Hol, W.G.J., Merritt, E.A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 119.15 kDa 
• Atom Count: 7,788 
• Modeled Residue Count: 921 
• Deposited Residue Count: 1,032 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate mutase	A, B, C, D	258	Plasmodium falciparum 3D7	Mutation(s): 1  Gene Names: PF11_0208 EC: 5.4.2.1 (PDB Primary Data), 5.4.2.11 (UniProt)
UniProt
Find proteins for Q8IIG6 (Plasmodium falciparum (isolate 3D7)) Explore Q8IIG6  Go to UniProtKB:  Q8IIG6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.236 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.062	α = 90
b = 76.12	β = 99.68
c = 101.68	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-17 
Deposition Author(s): Larson, E.T., Merritt, E.A., Medical Structural Genomics of Pathogenic Protozoa (MSGPP)

Revision History  

• Version 1.0: 2009-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description
• Version 1.5: 2025-10-22
  Changes: Structure summary