3MV4

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.167
R-Value Work: 0.146
R-Value Observed: 0.148

wwPDB Validation 3D Report Full Report

This is version 1.4 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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00436
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00437
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain GA [auth O] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth M] SDF format, chain W [auth N] SDF format, chain X [auth N] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth O] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth M] MOL2 format, chain W [auth N] MOL2 format, chain X [auth N]	G [auth A] GA [auth O] J [auth B] L [auth C] N [auth M] 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		Interactions Focus chain G [auth A] Focus chain GA [auth O] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth M] Focus chain W [auth N] Focus chain X [auth N] Interactions & Density Focus chain G [auth A] Focus chain GA [auth O] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth M] Focus chain W [auth N] Focus chain X [auth N]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth N] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain O [auth M] SDF format, chain Q [auth M] MOL2 format, chain AA [auth N] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth M] MOL2 format, chain Q [auth M]	AA [auth N] H [auth A] K [auth B] M [auth C] O [auth M] 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		Interactions Focus chain AA [auth N] Focus chain H [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth M] Focus chain Q [auth M] Interactions & Density Focus chain AA [auth N] Focus chain H [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth M] Focus chain Q [auth M]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain EA [auth N] SDF format, chain FA [auth N] SDF format, chain I [auth A] SDF format, chain JA [auth O] SDF format, chain KA [auth O] SDF format, chain LA [auth O] SDF format, chain R [auth M] SDF format, chain S [auth M] SDF format, chain T [auth M] SDF format, chain U [auth M] SDF format, chain Y [auth N] MOL2 format, chain EA [auth N] MOL2 format, chain FA [auth N] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth O] MOL2 format, chain KA [auth O] MOL2 format, chain LA [auth O] MOL2 format, chain R [auth M] MOL2 format, chain S [auth M] MOL2 format, chain T [auth M] MOL2 format, chain U [auth M] MOL2 format, chain Y [auth N]	EA [auth N] FA [auth N] I [auth A] JA [auth O] KA [auth O] 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		Interactions Focus chain EA [auth N] Focus chain FA [auth N] Focus chain I [auth A] Focus chain JA [auth O] Focus chain KA [auth O] Focus chain LA [auth O] Focus chain R [auth M] Focus chain S [auth M] Focus chain T [auth M] Focus chain U [auth M] Focus chain Y [auth N] Interactions & Density Focus chain EA [auth N] Focus chain FA [auth N] Focus chain I [auth A] Focus chain JA [auth O] Focus chain KA [auth O] Focus chain LA [auth O] Focus chain R [auth M] Focus chain S [auth M] Focus chain T [auth M] Focus chain U [auth M] Focus chain Y [auth N]
CO3 Query on CO3 Download Ideal Coordinates CCD File SDF format, chain BA [auth N] SDF format, chain CA [auth N] SDF format, chain DA [auth N] SDF format, chain IA [auth O] SDF format, chain V [auth M] MOL2 format, chain BA [auth N] MOL2 format, chain CA [auth N] MOL2 format, chain DA [auth N] MOL2 format, chain IA [auth O] MOL2 format, chain V [auth M]	BA [auth N], CA [auth N], DA [auth N], IA [auth O], V [auth M]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain BA [auth N] Focus chain CA [auth N] Focus chain DA [auth N] Focus chain IA [auth O] Focus chain V [auth M] Interactions & Density Focus chain BA [auth N] Focus chain CA [auth N] Focus chain DA [auth N] Focus chain IA [auth O] Focus chain V [auth M]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain HA [auth O] SDF format, chain P [auth M] SDF format, chain Z [auth N] MOL2 format, chain HA [auth O] MOL2 format, chain P [auth M] MOL2 format, chain Z [auth N]	HA [auth O], P [auth M], Z [auth N]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain HA [auth O] Focus chain P [auth M] Focus chain Z [auth N] Interactions & Density Focus chain HA [auth O] Focus chain P [auth M] Focus chain Z [auth N]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.167
R-Value Work: 0.146
R-Value Observed: 0.148
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-06-01

Deposition Author(s):

Purpero, V.M.

Lipscomb, J.D.

Revision History (Full details and data files)

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