3N3D | pdb_00003n3d

Crystal structure of geranylgeranyl pyrophosphate synthase from lactobacillus brevis atcc 367

• PDB DOI: https://doi.org/10.2210/pdb3N3D/pdb

• Classification: TRANSFERASE
• Organism(s): Levilactobacillus brevis ATCC 367
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-19 Released: 2010-06-02 
• Deposition Author(s): Patskovsky, Y., Toro, R., Rutter, M., Chang, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York Structural GenomiX Research Consortium (NYSGXRC), New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Literature

Crystal Structure of Geranylgeranyl Pyrophosphate Synthase from Lactobacillus Brevis

Patskovsky, Y., Toro, R., Rutter, M., Chang, S., 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: 76.13 kDa 
• Atom Count: 5,110 
• Modeled Residue Count: 635 
• Deposited Residue Count: 670 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranylgeranyl pyrophosphate synthase	A, B	335	Levilactobacillus brevis ATCC 367	Mutation(s): 0  Gene Names: LVIS_1638
UniProt
Find proteins for Q03Q08 (Levilactobacillus brevis (strain ATCC 367 / BCRC 12310 / CIP 105137 / JCM 1170 / LMG 11437 / NCIMB 947 / NCTC 947)) Explore Q03Q08  Go to UniProtKB:  Q03Q08

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.562	α = 90
b = 111.562	β = 90
c = 198.497	γ = 90

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: 2010-06-02 
Deposition Author(s): Patskovsky, Y., Toro, R., Rutter, M., Chang, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York Structural GenomiX Research Consortium (NYSGXRC), New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-06-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary
• 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: 2024-02-21
  Changes: Data collection, Database references