4WIU | pdb_00004wiu

Crystal Structure of PEPCK (Rv0211) from Mycobacterium tuberculosis in complex with oxalate and Mn2+

• PDB DOI: https://doi.org/10.2210/pdb4WIU/pdb

• Classification: LYASE,TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Ra
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-09-26 Released: 2014-10-22 
• Deposition Author(s): Kim, H.L., Sacchettini, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.195 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Literature

Crystal Structure of PEPCK (Rv0211) from Mycobacterium tuberculosis in complex with oxalate and Mn2+

Kim, H.L.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 67.78 kDa 
• Atom Count: 5,377 
• Modeled Residue Count: 600 
• Deposited Residue Count: 608 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoenolpyruvate carboxykinase [GTP]	A	608	Mycobacterium tuberculosis H37Ra	Mutation(s): 0  Gene Names: pckG, MRA_0219 EC: 4.1.1.32
UniProt
Find proteins for A5TYT6 (Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)) Explore A5TYT6  Go to UniProtKB:  A5TYT6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
OXL	C [auth A]	OXALATE ION C2 O4 MUBZPKHOEPUJKR-UHFFFAOYSA-L
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.195 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.969	α = 90
b = 122.739	β = 116.98
c = 64.697	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
PDB_EXTRACT	data extraction
HKL-2000	data scaling
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-22 
Deposition Author(s): Kim, H.L., Sacchettini, J.C.

Revision History  

• Version 1.0: 2014-10-22
  Type: Initial release
  
• Version 1.1: 2014-10-29
  Changes: Other, Structure summary
• Version 1.2: 2015-02-04
  Changes: Derived calculations
• Version 1.3: 2015-02-25
  Changes: Derived calculations
• Version 1.4: 2017-11-22
  Changes: Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
• Version 1.5: 2023-12-27
  Changes: Data collection, Database references, Refinement description