3LK5 | pdb_00003lk5

Crystal structure of putative Geranylgeranyl pyrophosphate synthase from Corynebacterium glutamicum

• PDB DOI: https://doi.org/10.2210/pdb3LK5/pdb

• Classification: TRANSFERASE
• Organism(s): Corynebacterium glutamicum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-01-27 Released: 2010-03-09 
• Deposition Author(s): Malashkevich, V.N., Toro, R., Patskovsky, Y., 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: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Crystal structure of putative Geranylgeranyl pyrophosphate synthase from Corynebacterium glutamicum Atcc 13032

Malashkevich, V.N., Toro, R., Patskovsky, Y., 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: 41.57 kDa 
• Atom Count: 2,740 
• Modeled Residue Count: 333 
• Deposited Residue Count: 380 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranylgeranyl pyrophosphate synthase	A	380	Corynebacterium glutamicum	Mutation(s): 0  Gene Names: Cgl2172 EC: 2.5.1.1
UniProt
Find proteins for Q8NNM1 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NNM1  Go to UniProtKB:  Q8NNM1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.434	α = 90
b = 125.434	β = 90
c = 52.067	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Malashkevich, V.N., Toro, R., Patskovsky, Y., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Structure summary