3S42

Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella enterica Typhimurium LT2 with Malonate and Boric Acid at the Active Site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal Structure of the 3-Dehydroquinate Dehydratase (aroD) from Salmonella enterica Typhimurium LT2 with Malonate and Boric Acid at the Active Site

Light, S.H.Minasov, G.Duban, M.-E.Halavaty, A.S.Krishna, S.N.Shuvalova, L.Kwon, K.Anderson, W.F.Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-dehydroquinate dehydratase
B, A
276Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Gene Names: aroD
EC: 4.2.1.10
Find proteins for P58687 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P58687
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BO3
Query on BO3

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Download CCD File 
A
BORIC ACID
B H3 O3
KGBXLFKZBHKPEV-UHFFFAOYSA-N
 Ligand Interaction
IMD
Query on IMD

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Download CCD File 
B
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
MLA
Query on MLA

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Download CCD File 
A, B
MALONIC ACID
DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A, B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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Download CCD File 
B
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.144 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.562α = 90.00
b = 72.569β = 90.00
c = 171.353γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Blu-Icedata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-10-29
    Type: Structure summary
  • Version 1.3: 2015-04-29
    Type: Non-polymer description
  • Version 1.4: 2017-11-08
    Type: Refinement description