3MV4 | pdb_00003mv4

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

• PDB DOI: https://doi.org/10.2210/pdb3MV4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-05-03 Released: 2011-06-01 
• Deposition Author(s): Purpero, V.M., Lipscomb, J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.167 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.146 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Hetero 24-mer - A12B12 Pseudo Symmetry: Tetrahedral - T  (Explore in 3D)
Pseudo Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 149.48 kDa 
• Atom Count: 12,660 
• Modeled Residue Count: 1,314 
• Deposited Residue Count: 1,314 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protocatechuate 3,4-dioxygenase alpha chain	A, B, C	200	Pseudomonas putida	Mutation(s): 0  Gene Names: pcaG, pcaH EC: 1.13.11.3
UniProt
Find proteins for P00436 (Pseudomonas putida) Explore P00436  Go to UniProtKB:  P00436

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protocatechuate 3,4-dioxygenase beta chain	D [auth M], E [auth N], F [auth O]	238	Pseudomonas putida	Mutation(s): 2  Gene Names: pcaH EC: 1.13.11.3
UniProt
Find proteins for P00437 (Pseudomonas putida) Explore P00437  Go to UniProtKB:  P00437

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], GA [auth O], J [auth B], L [auth C], N [auth M], W [auth N], X [auth N]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	AA [auth N], H [auth A], K [auth B], M [auth C], O [auth M], Q [auth M]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BME	EA [auth N], FA [auth N], I [auth A], JA [auth O], KA [auth O], LA [auth O], R [auth M], S [auth M], T [auth M], U [auth M], Y [auth N]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
CO3	BA [auth N], CA [auth N], DA [auth N], IA [auth O], V [auth M]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L
FE	HA [auth O], P [auth M], Z [auth N]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.167 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.146 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.311	α = 90
b = 140.487	β = 90
c = 168.061	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-01 
Deposition Author(s): Purpero, V.M., Lipscomb, J.D.

Revision History  

• Version 1.0: 2011-06-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Advisory, Refinement description
• Version 1.3: 2021-10-06
  Changes: Advisory, Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description