4LLS

Crystal structure of a farnesyl diphosphate synthase from Roseobacter denitrificans OCh 114, target EFI-509393, with IPP, GSPP, and calcium bound in active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of a farnesyl diphosphate synthase from Roseobacter denitrificans OCh 114, target EFI-509393, with IPP, GSPP and calcium bound in active site

Kim, J.Toro, R.Bhosle, R.Al Obaidi, N.F.Morisco, L.L.Wasserman, S.R.Sojitra, S.Washington, E.Scott Glenn, A.Chowdhury, S.Evans, B.Hammonds, J.Hillerich, B.Love, J.Seidel, R.D.Imker, H.J.Stead, M.Gerlt, J.A.Almo, S.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Geranyltranstransferase
A, B
311Roseobacter denitrificans OCh 114Mutation(s): 0 
Gene Names: ispARD1_0549
EC: 2.5.1.10
UniProt
Find proteins for Q16CN9 (Roseobacter denitrificans (strain ATCC 33942 / OCh 114))
Explore Q16CN9 
Go to UniProtKB:  Q16CN9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16CN9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GST
Query on GST

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
GERANYL S-THIOLODIPHOSPHATE
C10 H20 O6 P2 S
AKIXWSDUEPPMKM-JXMROGBWSA-N
IPE
Query on IPE

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
C5 H12 O7 P2
NUHSROFQTUXZQQ-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
J [auth B]
K [auth B]
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.095α = 90
b = 83.032β = 108.87
c = 71.386γ = 90
Software Package:
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2018-01-31
    Changes: Structure summary
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description