3MV6

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

PDB DOI: https://doi.org/10.2210/pdb3MV6/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: 1.86 Å
R-Value Free: 0.219
R-Value Work: 0.181
R-Value Observed: 0.183

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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: 149.01 kDa
Atom Count: 11,533
Modelled Residue Count: 1,314
Deposited Residue Count: 1,314
Unique protein chains: 2

Macromolecules

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(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

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(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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DHB Query on DHB Download Ideal Coordinates CCD File SDF format, chain CA [auth O] SDF format, chain S [auth M] SDF format, chain Y [auth N] MOL2 format, chain CA [auth O] MOL2 format, chain S [auth M] MOL2 format, chain Y [auth N]	CA [auth O], S [auth M], Y [auth N]	3,4-DIHYDROXYBENZOIC ACID C₇ H₆ O₄ YQUVCSBJEUQKSH-UHFFFAOYSA-N		Interactions Focus chain CA [auth O] Focus chain S [auth M] Focus chain Y [auth N] Interactions & Density Focus chain CA [auth O] Focus chain S [auth M] Focus chain Y [auth N]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain T [auth N] SDF format, chain Z [auth O] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain T [auth N] MOL2 format, chain Z [auth O]	G [auth A] H [auth A] J [auth B] K [auth B] N [auth C] G [auth A], H [auth A], J [auth B], K [auth B], N [auth C], T [auth N], Z [auth O]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain T [auth N] Focus chain Z [auth O] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain T [auth N] Focus chain Z [auth O]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth C] SDF format, chain P [auth C] MOL2 format, chain I [auth A] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C]	I [auth A], O [auth C], P [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain I [auth A] Focus chain O [auth C] Focus chain P [auth C]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth M] SDF format, chain U [auth N] SDF format, chain V [auth N] SDF format, chain W [auth N] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth M] MOL2 format, chain U [auth N] MOL2 format, chain V [auth N] MOL2 format, chain W [auth N]	L [auth B] M [auth B] Q [auth M] U [auth N] V [auth N] L [auth B], M [auth B], Q [auth M], U [auth N], V [auth N], W [auth N]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth M] Focus chain U [auth N] Focus chain V [auth N] Focus chain W [auth N] Interactions & Density Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth M] Focus chain U [auth N] Focus chain V [auth N] Focus chain W [auth N]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain BA [auth O] SDF format, chain R [auth M] SDF format, chain X [auth N] MOL2 format, chain BA [auth O] MOL2 format, chain R [auth M] MOL2 format, chain X [auth N]	BA [auth O], R [auth M], X [auth N]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain BA [auth O] Focus chain R [auth M] Focus chain X [auth N] Interactions & Density Focus chain BA [auth O] Focus chain R [auth M] Focus chain X [auth N]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth O] MOL2 format, chain AA [auth O]	AA [auth O]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth O] Interactions & Density Focus chain AA [auth O]