3MV6 | pdb_00003mv6

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 (Depositor), 0.219 (DCC)
R-Value Work:
0.181 (Depositor)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

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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
Modeled Residue Count: 1,314
Deposited Residue Count: 1,314
Unique protein chains: 2

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00436
Sequence Annotations Expand
Reference Sequence

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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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DHB Query on DHB Download:Ideal Coordinates CCD File SDF format, chain Y [auth N] SDF format, chain S [auth M] SDF format, chain CA [auth O] MOL2 format, chain Y [auth N] MOL2 format, chain S [auth M] MOL2 format, chain CA [auth O] mmCIF format, chain Y [auth N] mmCIF format, chain S [auth M] mmCIF format, chain CA [auth O]	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 Z [auth O] SDF format, chain T [auth N] SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain Z [auth O] MOL2 format, chain T [auth N] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain Z [auth O] mmCIF format, chain T [auth N] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	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 P [auth C] SDF format, chain O [auth C] MOL2 format, chain I [auth A] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] mmCIF format, chain I [auth A] mmCIF format, chain P [auth C] mmCIF format, chain O [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 U [auth N] SDF format, chain W [auth N] SDF format, chain V [auth N] SDF format, chain Q [auth M] SDF format, chain M [auth B] SDF format, chain L [auth B] MOL2 format, chain U [auth N] MOL2 format, chain W [auth N] MOL2 format, chain V [auth N] MOL2 format, chain Q [auth M] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] mmCIF format, chain U [auth N] mmCIF format, chain W [auth N] mmCIF format, chain V [auth N] mmCIF format, chain Q [auth M] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B]	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 X [auth N] SDF format, chain R [auth M] MOL2 format, chain BA [auth O] MOL2 format, chain X [auth N] MOL2 format, chain R [auth M] mmCIF format, chain BA [auth O] mmCIF format, chain X [auth N] mmCIF format, chain R [auth M]	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] mmCIF 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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.219 (Depositor), 0.219 (DCC)
R-Value Work: 0.181 (Depositor)
R-Value Observed: 0.183 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.142	α = 90
b = 140.831	β = 90
c = 167.83	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-06-01

Deposition Author(s):

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: Refinement description
Version 1.3: 2021-10-06
Changes: Database references, Derived calculations
Version 1.4: 2024-02-21
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.