3LXV | pdb_00003lxv

Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis

PDB DOI: https://doi.org/10.2210/pdb3LXV/pdb

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

Deposited: 2010-02-25 Released: 2011-03-09
Deposition Author(s): Purpero, V.M., Lipscomb, J.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.246 (Depositor), 0.255 (DCC)
R-Value Work:
0.201 (Depositor), 0.210 (DCC)
R-Value Observed:
0.203 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3LXV

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Tyrosine 447 of Protocatechuate 3,4-Dioxygenase Controls Efficient Progress Through Catalysis

Purpero, V.M., Valley, M.P., Ohlendorf, D.H., Lipscomb, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 150.52 kDa
Atom Count: 11,718
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, 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% 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	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00437
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4NC Query on 4NC Download:Ideal Coordinates CCD File SDF format, chain FA [auth N] SDF format, chain U [auth M] SDF format, chain UA [auth O] SDF format, chain WA [auth O] MOL2 format, chain FA [auth N] MOL2 format, chain U [auth M] MOL2 format, chain UA [auth O] MOL2 format, chain WA [auth O] mmCIF format, chain FA [auth N] mmCIF format, chain U [auth M] mmCIF format, chain UA [auth O] mmCIF format, chain WA [auth O]	FA [auth N], U [auth M], UA [auth O], WA [auth O]	4-NITROCATECHOL C₆ H₅ N O₄ XJNPNXSISMKQEX-UHFFFAOYSA-N		Interactions Focus chain FA [auth N] Focus chain U [auth M] Focus chain UA [auth O] Focus chain WA [auth O] Interactions & Density Focus chain FA [auth N] Focus chain U [auth M] Focus chain UA [auth O] Focus chain WA [auth O]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain SA [auth O] SDF format, chain X [auth B] MOL2 format, chain K [auth A] MOL2 format, chain SA [auth O] MOL2 format, chain X [auth B] mmCIF format, chain K [auth A] mmCIF format, chain SA [auth O] mmCIF format, chain X [auth B]	K [auth A], SA [auth O], X [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain K [auth A] Focus chain SA [auth O] Focus chain X [auth B] Interactions & Density Focus chain K [auth A] Focus chain SA [auth O] Focus chain X [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain V [auth B] SDF format, chain G [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain G [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain G [auth A]	G [auth A], IA [auth C], V [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain IA [auth C] Focus chain V [auth B] Interactions & Density Focus chain G [auth A] Focus chain IA [auth C] Focus chain V [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth N] SDF format, chain BA [auth N] SDF format, chain H [auth A] SDF format, chain JA [auth C] SDF format, chain N [auth M] SDF format, chain O [auth M] SDF format, chain Z [auth N] MOL2 format, chain AA [auth N] MOL2 format, chain BA [auth N] MOL2 format, chain H [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain N [auth M] MOL2 format, chain O [auth M] MOL2 format, chain Z [auth N] mmCIF format, chain AA [auth N] mmCIF format, chain BA [auth N] mmCIF format, chain H [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain N [auth M] mmCIF format, chain O [auth M] mmCIF format, chain Z [auth N]	AA [auth N] BA [auth N] H [auth A] JA [auth C] N [auth M] AA [auth N], BA [auth N], H [auth A], JA [auth C], N [auth M], O [auth M], Z [auth N]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth N] Focus chain BA [auth N] Focus chain H [auth A] Focus chain JA [auth C] Focus chain N [auth M] Focus chain O [auth M] Focus chain Z [auth N] Interactions & Density Focus chain AA [auth N] Focus chain BA [auth N] Focus chain H [auth A] Focus chain JA [auth C] Focus chain N [auth M] Focus chain O [auth M] Focus chain Z [auth N]
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain CA [auth N] SDF format, chain LA [auth C] SDF format, chain NA [auth O] SDF format, chain Q [auth M] SDF format, chain R [auth M] SDF format, chain RA [auth O] SDF format, chain W [auth B] SDF format, chain QA [auth O] SDF format, chain PA [auth O] SDF format, chain P [auth M] SDF format, chain OA [auth O] SDF format, chain KA [auth C] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain EA [auth N] MOL2 format, chain CA [auth N] MOL2 format, chain LA [auth C] MOL2 format, chain NA [auth O] MOL2 format, chain Q [auth M] MOL2 format, chain R [auth M] MOL2 format, chain RA [auth O] MOL2 format, chain W [auth B] MOL2 format, chain QA [auth O] MOL2 format, chain PA [auth O] MOL2 format, chain P [auth M] MOL2 format, chain OA [auth O] MOL2 format, chain KA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain EA [auth N] mmCIF format, chain CA [auth N] mmCIF format, chain LA [auth C] mmCIF format, chain NA [auth O] mmCIF format, chain Q [auth M] mmCIF format, chain R [auth M] mmCIF format, chain RA [auth O] mmCIF format, chain W [auth B] mmCIF format, chain QA [auth O] mmCIF format, chain PA [auth O] mmCIF format, chain P [auth M] mmCIF format, chain OA [auth O] mmCIF format, chain KA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain EA [auth N]	CA [auth N] EA [auth N] I [auth A] J [auth A] KA [auth C] CA [auth N], EA [auth N], I [auth A], J [auth A], KA [auth C], LA [auth C], NA [auth O], OA [auth O], P [auth M], PA [auth O], Q [auth M], QA [auth O], R [auth M], RA [auth O], W [auth B]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain CA [auth N] Focus chain EA [auth N] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain NA [auth O] Focus chain OA [auth O] Focus chain P [auth M] Focus chain PA [auth O] Focus chain Q [auth M] Focus chain QA [auth O] Focus chain R [auth M] Focus chain RA [auth O] Focus chain W [auth B] Interactions & Density Focus chain CA [auth N] Focus chain EA [auth N] Focus chain I [auth A] Focus chain J [auth A] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain NA [auth O] Focus chain OA [auth O] Focus chain P [auth M] Focus chain PA [auth O] Focus chain Q [auth M] Focus chain QA [auth O] Focus chain R [auth M] Focus chain RA [auth O] Focus chain W [auth B]
CO3 Query on CO3 Download:Ideal Coordinates CCD File SDF format, chain GA [auth N] SDF format, chain L [auth A] SDF format, chain MA [auth C] SDF format, chain S [auth M] SDF format, chain T [auth M] MOL2 format, chain GA [auth N] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain S [auth M] MOL2 format, chain T [auth M] mmCIF format, chain GA [auth N] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain S [auth M] mmCIF format, chain T [auth M]	GA [auth N], L [auth A], MA [auth C], S [auth M], T [auth M]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain GA [auth N] Focus chain L [auth A] Focus chain MA [auth C] Focus chain S [auth M] Focus chain T [auth M] Interactions & Density Focus chain GA [auth N] Focus chain L [auth A] Focus chain MA [auth C] Focus chain S [auth M] Focus chain T [auth M]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain DA [auth N] SDF format, chain M SDF format, chain VA [auth O] MOL2 format, chain DA [auth N] MOL2 format, chain M MOL2 format, chain VA [auth O] mmCIF format, chain DA [auth N] mmCIF format, chain M mmCIF format, chain VA [auth O]	DA [auth N], M, VA [auth O]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain DA [auth N] Focus chain M Focus chain VA [auth O] Interactions & Density Focus chain DA [auth N] Focus chain M Focus chain VA [auth O]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain HA [auth N] SDF format, chain TA [auth O] SDF format, chain Y [auth B] MOL2 format, chain HA [auth N] MOL2 format, chain TA [auth O] MOL2 format, chain Y [auth B] mmCIF format, chain HA [auth N] mmCIF format, chain TA [auth O] mmCIF format, chain Y [auth B]	HA [auth N], TA [auth O], Y [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain HA [auth N] Focus chain TA [auth O] Focus chain Y [auth B] Interactions & Density Focus chain HA [auth N] Focus chain TA [auth O] Focus chain Y [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.246 (Depositor), 0.255 (DCC)
R-Value Work: 0.201 (Depositor), 0.210 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.11	α = 90
b = 140.59	β = 90
c = 167.96	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
d*TREK	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-03-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-03-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-10-13
Changes: Database references, Derived calculations
Version 1.3: 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.