3LMD

Crystal structure of geranylgeranyl pyrophosphate synthase from corynebacterium glutamicum atcc 13032

• PDB DOI: https://doi.org/10.2210/pdb3LMD/pdb

• Classification: TRANSFERASE
• Organism(s): Corynebacterium glutamicum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-01-29 Released: 2010-02-16 
• Deposition Author(s): Patskovsky, Y., Ho, M., Toro, R., Rutter, M., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.214 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 

Literature

Crystal Structure of Geranylgeranyl Pyrophosphate Synthase from Corynebacterium Glutamicum

Patskovsky, Y., Ho, M., Toro, R., Rutter, M., Sauder, J.M., Burley, S.K., Almo, S.C.

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: 39.08 kDa 
• Atom Count: 2,605 
• Modelled Residue Count: 317 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranylgeranyl pyrophosphate synthase	A	360	Corynebacterium glutamicum	Mutation(s): 0  Gene Names: ispB, Cgl0473, cg0559 EC: 2.5.1.30
UniProt
Find proteins for Q8NT37 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NT37  Go to UniProtKB:  Q8NT37

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.214 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.548	α = 90
b = 71.548	β = 90
c = 151.322	γ = 120

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-16 
Deposition Author(s): Patskovsky, Y., Ho, M., Toro, R., Rutter, M., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references