3LMX | pdb_00003lmx

Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis

PDB DOI: https://doi.org/10.2210/pdb3LMX/pdb

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

Deposited: 2010-02-01 Released: 2011-02-16
Deposition Author(s): Purpero, V.M., Lipscomb, J.D., Shi, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.213 (Depositor), 0.210 (DCC)
R-Value Work:
0.169 (Depositor), 0.168 (DCC)
R-Value Observed:
0.171 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3LMX

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Tyrosine 447 of Protocatechuate 34,-Dioxygenase Controls Efficient Progress Through Catalysis

Purpero, V.M., Lipscomb, J.D., Ohlendorf, D.H., Shi, K., Dolbeare, K.B., Brown, C.K., Burk, D.

To be published.

Macromolecule Content

Total Structure Weight: 151.93 kDa
Atom Count: 11,263
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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DHB Query on DHB Download:Ideal Coordinates CCD File SDF format, chain JA [auth N] SDF format, chain P [auth M] SDF format, chain R [auth M] SDF format, chain Q [auth M] SDF format, chain KA [auth N] SDF format, chain DB [auth O] MOL2 format, chain JA [auth N] MOL2 format, chain P [auth M] MOL2 format, chain R [auth M] MOL2 format, chain Q [auth M] MOL2 format, chain KA [auth N] MOL2 format, chain DB [auth O] mmCIF format, chain JA [auth N] mmCIF format, chain P [auth M] mmCIF format, chain R [auth M] mmCIF format, chain Q [auth M] mmCIF format, chain KA [auth N] mmCIF format, chain DB [auth O]	DB [auth O] JA [auth N] KA [auth N] P [auth M] Q [auth M] DB [auth O], JA [auth N], KA [auth N], P [auth M], Q [auth M], R [auth M]	3,4-DIHYDROXYBENZOIC ACID C₇ H₆ O₄ YQUVCSBJEUQKSH-UHFFFAOYSA-N		Interactions Focus chain DB [auth O] Focus chain JA [auth N] Focus chain KA [auth N] Focus chain P [auth M] Focus chain Q [auth M] Focus chain R [auth M] Interactions & Density Focus chain DB [auth O] Focus chain JA [auth N] Focus chain KA [auth N] Focus chain P [auth M] Focus chain Q [auth M] Focus chain R [auth M]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain FB [auth O] SDF format, chain NA [auth N] SDF format, chain PA [auth N] SDF format, chain V [auth M] SDF format, chain WA [auth C] SDF format, chain ZA [auth C] SDF format, chain YA [auth C] SDF format, chain XA [auth C] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain GA [auth B] MOL2 format, chain FB [auth O] MOL2 format, chain NA [auth N] MOL2 format, chain PA [auth N] MOL2 format, chain V [auth M] MOL2 format, chain WA [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth B] mmCIF format, chain FB [auth O] mmCIF format, chain NA [auth N] mmCIF format, chain PA [auth N] mmCIF format, chain V [auth M] mmCIF format, chain WA [auth C] mmCIF format, chain ZA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain XA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth B]	FB [auth O] GA [auth B] H [auth A] I [auth A] NA [auth N] FB [auth O], GA [auth B], H [auth A], I [auth A], NA [auth N], PA [auth N], V [auth M], WA [auth C], XA [auth C], YA [auth C], ZA [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain FB [auth O] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain NA [auth N] Focus chain PA [auth N] Focus chain V [auth M] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain FB [auth O] Focus chain GA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain NA [auth N] Focus chain PA [auth N] Focus chain V [auth M] Focus chain WA [auth C] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain ZA [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain JB [auth O] SDF format, chain LA [auth N] SDF format, chain S [auth M] SDF format, chain T [auth M] SDF format, chain UA [auth N] SDF format, chain U [auth M] SDF format, chain OA [auth N] SDF format, chain MA [auth N] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain JB [auth O] MOL2 format, chain LA [auth N] MOL2 format, chain S [auth M] MOL2 format, chain T [auth M] MOL2 format, chain UA [auth N] MOL2 format, chain U [auth M] MOL2 format, chain OA [auth N] MOL2 format, chain MA [auth N] mmCIF format, chain FA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain JB [auth O] mmCIF format, chain LA [auth N] mmCIF format, chain S [auth M] mmCIF format, chain T [auth M] mmCIF format, chain UA [auth N] mmCIF format, chain U [auth M] mmCIF format, chain OA [auth N] mmCIF format, chain MA [auth N]	FA [auth B] G [auth A] JB [auth O] LA [auth N] MA [auth N] FA [auth B], G [auth A], JB [auth O], LA [auth N], MA [auth N], OA [auth N], S [auth M], T [auth M], U [auth M], UA [auth N]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain FA [auth B] Focus chain G [auth A] Focus chain JB [auth O] Focus chain LA [auth N] Focus chain MA [auth N] Focus chain OA [auth N] Focus chain S [auth M] Focus chain T [auth M] Focus chain U [auth M] Focus chain UA [auth N] Interactions & Density Focus chain FA [auth B] Focus chain G [auth A] Focus chain JB [auth O] Focus chain LA [auth N] Focus chain MA [auth N] Focus chain OA [auth N] Focus chain S [auth M] Focus chain T [auth M] Focus chain U [auth M] Focus chain UA [auth N]
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain BB [auth C] SDF format, chain HA [auth B] SDF format, chain N [auth A] SDF format, chain TA [auth N] SDF format, chain Z [auth M] SDF format, chain X [auth M] SDF format, chain W [auth M] SDF format, chain VA [auth N] SDF format, chain RA [auth N] SDF format, chain QA [auth N] SDF format, chain MB [auth O] SDF format, chain M [auth A] SDF format, chain LB [auth O] SDF format, chain KB [auth O] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain HB [auth O] SDF format, chain GB [auth O] SDF format, chain EB [auth O] SDF format, chain EA [auth M] SDF format, chain DA [auth M] SDF format, chain CA [auth M] SDF format, chain BA [auth M] MOL2 format, chain BB [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain TA [auth N] MOL2 format, chain Z [auth M] MOL2 format, chain X [auth M] MOL2 format, chain W [auth M] MOL2 format, chain VA [auth N] MOL2 format, chain RA [auth N] MOL2 format, chain QA [auth N] MOL2 format, chain MB [auth O] MOL2 format, chain M [auth A] MOL2 format, chain LB [auth O] MOL2 format, chain KB [auth O] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain HB [auth O] MOL2 format, chain GB [auth O] MOL2 format, chain EB [auth O] MOL2 format, chain EA [auth M] MOL2 format, chain DA [auth M] MOL2 format, chain CA [auth M] MOL2 format, chain BA [auth M] mmCIF format, chain BB [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain TA [auth N] mmCIF format, chain Z [auth M] mmCIF format, chain X [auth M] mmCIF format, chain W [auth M] mmCIF format, chain VA [auth N] mmCIF format, chain RA [auth N] mmCIF format, chain QA [auth N] mmCIF format, chain MB [auth O] mmCIF format, chain M [auth A] mmCIF format, chain LB [auth O] mmCIF format, chain KB [auth O] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain HB [auth O] mmCIF format, chain GB [auth O] mmCIF format, chain EB [auth O] mmCIF format, chain EA [auth M] mmCIF format, chain DA [auth M] mmCIF format, chain CA [auth M] mmCIF format, chain BA [auth M]	BA [auth M] BB [auth C] CA [auth M] DA [auth M] EA [auth M] BA [auth M], BB [auth C], CA [auth M], DA [auth M], EA [auth M], EB [auth O], GB [auth O], HA [auth B], HB [auth O], J [auth A], K [auth A], KB [auth O], LB [auth O], M [auth A], MB [auth O], N [auth A], QA [auth N], RA [auth N], TA [auth N], VA [auth N], W [auth M], X [auth M], Z [auth M]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain BA [auth M] Focus chain BB [auth C] Focus chain CA [auth M] Focus chain DA [auth M] Focus chain EA [auth M] Focus chain EB [auth O] Focus chain GB [auth O] Focus chain HA [auth B] Focus chain HB [auth O] Focus chain J [auth A] Focus chain K [auth A] Focus chain KB [auth O] Focus chain LB [auth O] Focus chain M [auth A] Focus chain MB [auth O] Focus chain N [auth A] Focus chain QA [auth N] Focus chain RA [auth N] Focus chain TA [auth N] Focus chain VA [auth N] Focus chain W [auth M] Focus chain X [auth M] Focus chain Z [auth M] Interactions & Density Focus chain BA [auth M] Focus chain BB [auth C] Focus chain CA [auth M] Focus chain DA [auth M] Focus chain EA [auth M] Focus chain EB [auth O] Focus chain GB [auth O] Focus chain HA [auth B] Focus chain HB [auth O] Focus chain J [auth A] Focus chain K [auth A] Focus chain KB [auth O] Focus chain LB [auth O] Focus chain M [auth A] Focus chain MB [auth O] Focus chain N [auth A] Focus chain QA [auth N] Focus chain RA [auth N] Focus chain TA [auth N] Focus chain VA [auth N] Focus chain W [auth M] Focus chain X [auth M] Focus chain Z [auth M]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain O [auth M] SDF format, chain IA [auth N] SDF format, chain CB [auth O] MOL2 format, chain O [auth M] MOL2 format, chain IA [auth N] MOL2 format, chain CB [auth O] mmCIF format, chain O [auth M] mmCIF format, chain IA [auth N] mmCIF format, chain CB [auth O]	CB [auth O], IA [auth N], O [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain CB [auth O] Focus chain IA [auth N] Focus chain O [auth M] Interactions & Density Focus chain CB [auth O] Focus chain IA [auth N] Focus chain O [auth M]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain AB [auth C] SDF format, chain L [auth A] SDF format, chain Y [auth M] SDF format, chain SA [auth N] SDF format, chain IB [auth O] SDF format, chain AA [auth M] MOL2 format, chain AB [auth C] MOL2 format, chain L [auth A] MOL2 format, chain Y [auth M] MOL2 format, chain SA [auth N] MOL2 format, chain IB [auth O] MOL2 format, chain AA [auth M] mmCIF format, chain AB [auth C] mmCIF format, chain L [auth A] mmCIF format, chain Y [auth M] mmCIF format, chain SA [auth N] mmCIF format, chain IB [auth O] mmCIF format, chain AA [auth M]	AA [auth M] AB [auth C] IB [auth O] L [auth A] SA [auth N] AA [auth M], AB [auth C], IB [auth O], L [auth A], SA [auth N], Y [auth M]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth M] Focus chain AB [auth C] Focus chain IB [auth O] Focus chain L [auth A] Focus chain SA [auth N] Focus chain Y [auth M] Interactions & Density Focus chain AA [auth M] Focus chain AB [auth C] Focus chain IB [auth O] Focus chain L [auth A] Focus chain SA [auth N] Focus chain Y [auth M]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.213 (Depositor), 0.210 (DCC)
R-Value Work: 0.169 (Depositor), 0.168 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.982	α = 90
b = 140.578	β = 90
c = 167.824	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-02-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-02-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2021-10-13
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.