5DEI

BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.136 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA

Bera, A.K.Hasson, M.S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Benzoylformate decarboxylase
A, B, C, D
524Pseudomonas putidaMutation(s): 0 
Gene Names: mdlC
EC: 4.1.1.7
UniProt
Find proteins for P20906 (Pseudomonas putida)
Explore P20906 
Go to UniProtKB:  P20906
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20906
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TPP
Query on TPP

Download Ideal Coordinates CCD File 
F [auth A],
M [auth B],
U [auth C],
X [auth D]
THIAMINE DIPHOSPHATE
C12 H19 N4 O7 P2 S
AYEKOFBPNLCAJY-UHFFFAOYSA-O
BCT
Query on BCT

Download Ideal Coordinates CCD File 
E [auth A],
L [auth B],
T [auth C],
W [auth D]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
R [auth B]
S [auth B]
V [auth C]
J [auth A],
K [auth A],
R [auth B],
S [auth B],
V [auth C],
Z [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

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G [auth A]
H [auth A]
I [auth A]
N [auth B]
O [auth B]
G [auth A],
H [auth A],
I [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
Y [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.136 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.166α = 63.59
b = 92.451β = 72.42
c = 93.715γ = 72.88
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-16
    Type: Initial release
  • Version 2.0: 2021-08-04
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-09-27
    Changes: Data collection, Database references, Refinement description