4LFE | pdb_00004lfe

Crystal structure of geranylgeranyl diphosphate synthase sub1274 (target efi-509455) from streptococcus uberis 0140j with bound magnesium and isopentyl diphosphate, partially liganded complex;

• PDB DOI: https://doi.org/10.2210/pdb4LFE/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus uberis 0140J
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-06-26 Released: 2013-07-10 
• Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Imker, H.J., Al Obaidi, N., Stead, M., Love, J., Poulter, C.D., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.236 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Geranylgeranyl Diphosphate Synthase from Streptococcus Uberis 0140J

Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Imker, H.J., Al Obaidi, N., Stead, M., Love, J., Poulter, C.D., Gerlt, J.A., 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: 65.46 kDa 
• Atom Count: 4,662 
• Modeled Residue Count: 562 
• Deposited Residue Count: 580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranylgeranyl diphosphate synthase	A, B	290	Streptococcus uberis 0140J	Mutation(s): 0  Gene Names: fps, SUB1274 EC: 2.5.1.10
UniProt
Find proteins for B9DUT7 (Streptococcus uberis (strain ATCC BAA-854 / 0140J)) Explore B9DUT7  Go to UniProtKB:  B9DUT7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPE	C [auth A], F [auth B], G [auth B]	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE C5 H12 O7 P2 NUHSROFQTUXZQQ-UHFFFAOYSA-N
MG	D [auth A], E [auth A], H [auth B], I [auth B], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.236 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.798	α = 90
b = 75.789	β = 90
c = 124.62	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-10 
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Imker, H.J., Al Obaidi, N., Stead, M., Love, J., Poulter, C.D., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2013-07-10
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description