3MFL

Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.157 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Axial Ligand Swapping In Double Mutant Maintains Intradiol-cleavage Chemistry in Protocatechuate 3,4-Dioxygenase

Purpero, V.M.Lipscomb, J.D.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protocatechuate 3,4-dioxygenase alpha chain
A, B, C
200Pseudomonas putidaMutation(s): 0 
Gene Names: pcaG
EC: 1.13.11.3
Find proteins for P00436 (Pseudomonas putida)
Go to UniProtKB:  P00436
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protocatechuate 3,4-dioxygenase beta chain
M, N, O
238Pseudomonas putidaMutation(s): 2 
Gene Names: pcaH
EC: 1.13.11.3
Find proteins for P00437 (Pseudomonas putida)
Go to UniProtKB:  P00437
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DHY
Query on DHY

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Download CCD File 
M, N, O
2-(3,4-DIHYDROXYPHENYL)ACETIC ACID
C8 H8 O4
CFFZDZCDUFSOFZ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B, C, N
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
O
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B, C, N, O
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

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Download CCD File 
A, B
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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Download CCD File 
M, N, O
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CO3
Query on CO3

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Download CCD File 
M
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.157 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 128.319α = 90.00
b = 140.769β = 90.00
c = 168.183γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
DENZOdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description