3T63 | pdb_00003t63

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

PDB DOI: https://doi.org/10.2210/pdb3T63/pdb

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

Deposited: 2011-07-28 Released: 2012-08-01
Deposition Author(s): Purpero, V.M., Lipscomb, J.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free:
0.178 (Depositor), 0.181 (DCC)
R-Value Work:
0.155 (Depositor)
R-Value Observed:
0.156 (Depositor)

Starting Model: experimental
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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.

Macromolecule Content

Total Structure Weight: 148.58 kDa
Atom Count: 12,175
Modeled Residue Count: 1,314
Deposited Residue Count: 1,314
Unique protein chains: 2

Macromolecules

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| 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 EC: 1.13.11.3
UniProt
Find proteins for P00436 (Pseudomonas putida) Explore P00436 Go to UniProtKB: P00436
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00436
Sequence Annotations Expand
Reference Sequence

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00437
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.178 (Depositor), 0.181 (DCC)
R-Value Work: 0.155 (Depositor)
R-Value Observed: 0.156 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.119	α = 90
b = 140.618	β = 90
c = 167.879	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-08-01

Deposition Author(s):

Purpero, V.M.

Lipscomb, J.D.

Revision History (Full details and data files)

Version 1.0: 2012-08-01
Type: Initial release
Version 1.1: 2017-11-08
Changes: Advisory, Refinement description
Version 1.2: 2023-09-13
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description