3MI1

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

PDB DOI: https://doi.org/10.2210/pdb3MI1/pdb

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

Deposited: 2010-04-09 Released: 2011-04-27
Deposition Author(s): Purpero, V.M., Lipscomb, J.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.174
R-Value Work: 0.148
R-Value Observed: 0.149

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: 149.3 kDa
Atom Count: 12,179
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, C [auth B], E [auth C]	200	Pseudomonas putida	Mutation(s): 0 Gene Names: pcaG 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	B [auth M], D [auth N], F [auth O]	238	Pseudomonas putida	Mutation(s): 1 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 I [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain T [auth N] SDF format, chain X [auth C] SDF format, chain Y [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth O] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth N] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth O] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth N] mmCIF format, chain X [auth C] mmCIF format, chain Y [auth C]	G [auth A] GA [auth O] I [auth A] P [auth B] Q [auth B] G [auth A], GA [auth O], I [auth A], P [auth B], Q [auth B], T [auth N], X [auth C], Y [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain GA [auth O] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth N] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain G [auth A] Focus chain GA [auth O] Focus chain I [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth N] Focus chain X [auth C] Focus chain Y [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain DA [auth O] SDF format, chain H [auth A] SDF format, chain K [auth M] SDF format, chain R [auth B] SDF format, chain V [auth N] SDF format, chain Z [auth C] MOL2 format, chain DA [auth O] MOL2 format, chain H [auth A] MOL2 format, chain K [auth M] MOL2 format, chain R [auth B] MOL2 format, chain V [auth N] MOL2 format, chain Z [auth C] mmCIF format, chain DA [auth O] mmCIF format, chain H [auth A] mmCIF format, chain K [auth M] mmCIF format, chain R [auth B] mmCIF format, chain V [auth N] mmCIF format, chain Z [auth C]	DA [auth O] H [auth A] K [auth M] R [auth B] V [auth N] DA [auth O], H [auth A], K [auth M], R [auth B], V [auth N], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain DA [auth O] Focus chain H [auth A] Focus chain K [auth M] Focus chain R [auth B] Focus chain V [auth N] Focus chain Z [auth C] Interactions & Density Focus chain DA [auth O] Focus chain H [auth A] Focus chain K [auth M] Focus chain R [auth B] Focus chain V [auth N] Focus chain Z [auth C]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain EA [auth O] SDF format, chain FA [auth O] SDF format, chain IA [auth O] SDF format, chain M SDF format, chain N [auth M] SDF format, chain U [auth N] SDF format, chain W [auth N] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain EA [auth O] MOL2 format, chain FA [auth O] MOL2 format, chain IA [auth O] MOL2 format, chain M MOL2 format, chain N [auth M] MOL2 format, chain U [auth N] MOL2 format, chain W [auth N] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain EA [auth O] mmCIF format, chain FA [auth O] mmCIF format, chain IA [auth O] mmCIF format, chain M mmCIF format, chain N [auth M] mmCIF format, chain U [auth N] mmCIF format, chain W [auth N]	AA [auth C] BA [auth C] EA [auth O] FA [auth O] IA [auth O] AA [auth C], BA [auth C], EA [auth O], FA [auth O], IA [auth O], M, N [auth M], U [auth N], W [auth N]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain EA [auth O] Focus chain FA [auth O] Focus chain IA [auth O] Focus chain M Focus chain N [auth M] Focus chain U [auth N] Focus chain W [auth N] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain EA [auth O] Focus chain FA [auth O] Focus chain IA [auth O] Focus chain M Focus chain N [auth M] Focus chain U [auth N] Focus chain W [auth N]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain CA [auth O] SDF format, chain J [auth M] SDF format, chain S [auth N] MOL2 format, chain CA [auth O] MOL2 format, chain J [auth M] MOL2 format, chain S [auth N] mmCIF format, chain CA [auth O] mmCIF format, chain J [auth M] mmCIF format, chain S [auth N]	CA [auth O], J [auth M], S [auth N]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain CA [auth O] Focus chain J [auth M] Focus chain S [auth N] Interactions & Density Focus chain CA [auth O] Focus chain J [auth M] Focus chain S [auth N]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain HA [auth O] SDF format, chain L [auth M] SDF format, chain O [auth M] MOL2 format, chain HA [auth O] MOL2 format, chain L [auth M] MOL2 format, chain O [auth M] mmCIF format, chain HA [auth O] mmCIF format, chain L [auth M] mmCIF format, chain O [auth M]	HA [auth O], L [auth M], O [auth M]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain HA [auth O] Focus chain L [auth M] Focus chain O [auth M] Interactions & Density Focus chain HA [auth O] Focus chain L [auth M] Focus chain O [auth M]