2QIW | pdb_00002qiw

Crystal structure of a putative phosphoenolpyruvate phosphonomutase (ncgl1015, cgl1060) from corynebacterium glutamicum atcc 13032 at 1.80 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2QIW/pdb

• Classification: TRANSFERASE
• Organism(s): Corynebacterium glutamicum ATCC 13032
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-07-05 Released: 2007-07-17 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.168 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Literature

Crystal structure of putative PEP phosphonomutase (NP_600288.1) from Corynebacterium glutamicum ATCC 13032 Kitasato at 1.80 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 55.33 kDa 
• Atom Count: 4,433 
• Modeled Residue Count: 510 
• Deposited Residue Count: 510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEP phosphonomutase	A, B	255	Corynebacterium glutamicum ATCC 13032	Mutation(s): 5  Gene Names: NP_600288.1, Cgl1060 EC: 2.7.8.23
UniProt
Find proteins for Q8NRI8 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NRI8  Go to UniProtKB:  Q8NRI8

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	O [auth B]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
SO4	C [auth A], M [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], P [auth B], Q [auth B], R [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	N [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNL	D [auth A]	Unknown ligand VEXZGXHMUGYJMC-UHFFFAOYSA-M

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: 1.80 Å
• R-Value Free:  0.168 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M32QIW

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.52	α = 90
b = 94.56	β = 90
c = 107.97	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-17 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2007-07-17
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.5: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.6: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary