6MWF

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0459


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.151 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF) Burkholderia pseudomallei in complex with ligand HGN-0456.

Abendroth, J.Dranow, D.M.Pierce, P.G.Horn, J.R.Hagen, T.J.Lorimer, D.D.Horanyi, P.S.Edwards, T.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
A, B, C
166Burkholderia pseudomallei 1710bMutation(s): 0 
Gene Names: ispFBURPS1710b_2511
EC: 4.6.1.12
UniProt
Find proteins for Q3JRA0 (Burkholderia pseudomallei (strain 1710b))
Explore Q3JRA0 
Go to UniProtKB:  Q3JRA0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3JRA0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SFY (Subject of Investigation/LOI)
Query on SFY

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E [auth A],
J [auth C]
4-amino-N-(pyridin-2-yl)benzenesulfonamide
C11 H11 N3 O2 S
GECHUMIMRBOMGK-UHFFFAOYSA-N
DMS
Query on DMS

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F [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

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D [auth A],
H [auth B],
I [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

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G [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.03α = 90
b = 67.93β = 96.58
c = 60.76γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references
  • Version 1.2: 2020-03-11
    Changes: Data collection
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description