4QRO

CRYSTAL STRUCTURE of DIHYDROXYBENZOIC ACID DECARBBOXYLASE BPRO_2061 (TARGET EFI-500288) FROM POLAROMONAS SP. JS666 WITH BOUND MANGANESE AND AN INHIBITOR, 2-NITRORESORCINOL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Dihydroxybenzoate Decarboxylase from Frompolaromonas Sp WITH BOUND MANGANESE AND 2-NITRORESORCINOL

Patskovsky, Y.Vladimirova, A.Toro, R.Bhosle, R.Raushel, F.M.Almo, S.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-resorcylate decarboxylase
A, B, C, D, E
A, B, C, D, E, F, G, H
348Polaromonas sp. JS666Mutation(s): 0 
Gene Names: Bpro_2061
UniProt
Find proteins for Q12BV1 (Polaromonas sp. (strain JS666 / ATCC BAA-500))
Explore Q12BV1 
Go to UniProtKB:  Q12BV1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12BV1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
38L
Query on 38L

Download Ideal Coordinates CCD File 
CA [auth E]
GA [auth F]
JA [auth G]
M [auth A]
PA [auth H]
CA [auth E],
GA [auth F],
JA [auth G],
M [auth A],
PA [auth H],
Q [auth B],
V [auth C],
Y [auth D]
2-nitrobenzene-1,3-diol
C6 H5 N O4
ZLCPKMIJYMHZMJ-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
DA [auth F]
I [auth A]
J [auth A]
LA [auth H]
N [auth B]
DA [auth F],
I [auth A],
J [auth A],
LA [auth H],
N [auth B],
R [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT
Query on BCT

Download Ideal Coordinates CCD File 
KA [auth G]BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
FA [auth F]
IA [auth G]
L [auth A]
AA [auth E],
BA [auth E],
FA [auth F],
IA [auth G],
L [auth A],
NA [auth H],
OA [auth H],
P [auth B],
T [auth C],
U [auth C],
X [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MN
Query on MN

Download Ideal Coordinates CCD File 
EA [auth F]
HA [auth G]
K [auth A]
MA [auth H]
O [auth B]
EA [auth F],
HA [auth G],
K [auth A],
MA [auth H],
O [auth B],
S [auth C],
W [auth D],
Z [auth E]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.958α = 90
b = 151.058β = 92.15
c = 143.826γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description