3LKT | pdb_00003lkt

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

PDB DOI: https://doi.org/10.2210/pdb3LKT/pdb

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

Deposited: 2010-01-27 Released: 2011-02-23
Deposition Author(s): Lipscomb, J.D., Purpero, V.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.173 (Depositor), 0.178 (DCC)
R-Value Work:
0.148 (Depositor), 0.153 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

This is version 1.5 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., Burk, D., Dolbeare, K.B., Brown, K.C.

To be published.

Macromolecule Content

Total Structure Weight: 298.23 kDa
Atom Count: 23,995
Modeled Residue Count: 2,628
Deposited Residue Count: 2,628
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 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] G [auth D] I [auth E] A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	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

Find similar proteins by:

| 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] H [auth P] J [auth Q] B [auth M], D [auth N], F [auth O], H [auth P], J [auth Q], L [auth R]	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
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain FB [auth E] SDF format, chain NB [auth F] SDF format, chain O [auth A] SDF format, chain TA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain FB [auth E] MOL2 format, chain NB [auth F] MOL2 format, chain O [auth A] MOL2 format, chain TA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain FB [auth E] mmCIF format, chain NB [auth F] mmCIF format, chain O [auth A] mmCIF format, chain TA [auth D]	AA [auth B], FB [auth E], NB [auth F], O [auth A], TA [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain AA [auth B] Focus chain FB [auth E] Focus chain NB [auth F] Focus chain O [auth A] Focus chain TA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain FB [auth E] Focus chain NB [auth F] Focus chain O [auth A] Focus chain TA [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain EB [auth E] SDF format, chain HA [auth C] SDF format, chain M [auth A] SDF format, chain MB [auth F] SDF format, chain SA [auth D] SDF format, chain Z [auth B] MOL2 format, chain EB [auth E] MOL2 format, chain HA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MB [auth F] MOL2 format, chain SA [auth D] MOL2 format, chain Z [auth B] mmCIF format, chain EB [auth E] mmCIF format, chain HA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain MB [auth F] mmCIF format, chain SA [auth D] mmCIF format, chain Z [auth B]	EB [auth E] HA [auth C] M [auth A] MB [auth F] SA [auth D] EB [auth E], HA [auth C], M [auth A], MB [auth F], SA [auth D], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EB [auth E] Focus chain HA [auth C] Focus chain M [auth A] Focus chain MB [auth F] Focus chain SA [auth D] Focus chain Z [auth B] Interactions & Density Focus chain EB [auth E] Focus chain HA [auth C] Focus chain M [auth A] Focus chain MB [auth F] Focus chain SA [auth D] Focus chain Z [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain IA [auth C] SDF format, chain U [auth M] MOL2 format, chain IA [auth C] MOL2 format, chain U [auth M] mmCIF format, chain IA [auth C] mmCIF format, chain U [auth M]	IA [auth C], U [auth M]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain IA [auth C] Focus chain U [auth M] Interactions & Density Focus chain IA [auth C] Focus chain U [auth M]
BME Query on BME Download:Ideal Coordinates CCD File SDF format, chain AB [auth P] SDF format, chain BB [auth P] SDF format, chain CB [auth P] SDF format, chain DA [auth N] SDF format, chain DB [auth P] SDF format, chain EA [auth N] SDF format, chain FA [auth N] SDF format, chain GA [auth N] SDF format, chain IB [auth Q] SDF format, chain JA [auth C] SDF format, chain JB [auth Q] SDF format, chain KB [auth Q] SDF format, chain LB [auth Q] SDF format, chain MA [auth O] SDF format, chain N [auth A] SDF format, chain NA [auth O] SDF format, chain OA [auth O] SDF format, chain PA [auth O] SDF format, chain QA [auth O] SDF format, chain QB [auth R] SDF format, chain RA [auth O] SDF format, chain RB [auth R] SDF format, chain SB [auth R] SDF format, chain TB [auth R] SDF format, chain V [auth M] SDF format, chain W [auth M] SDF format, chain WA [auth P] SDF format, chain X [auth M] SDF format, chain XA [auth P] SDF format, chain Y [auth M] SDF format, chain YA [auth P] SDF format, chain ZA [auth P] MOL2 format, chain AB [auth P] MOL2 format, chain BB [auth P] MOL2 format, chain CB [auth P] MOL2 format, chain DA [auth N] MOL2 format, chain DB [auth P] MOL2 format, chain EA [auth N] MOL2 format, chain FA [auth N] MOL2 format, chain GA [auth N] MOL2 format, chain IB [auth Q] MOL2 format, chain JA [auth C] MOL2 format, chain JB [auth Q] MOL2 format, chain KB [auth Q] MOL2 format, chain LB [auth Q] MOL2 format, chain MA [auth O] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth O] MOL2 format, chain OA [auth O] MOL2 format, chain PA [auth O] MOL2 format, chain QA [auth O] MOL2 format, chain QB [auth R] MOL2 format, chain RA [auth O] MOL2 format, chain RB [auth R] MOL2 format, chain SB [auth R] MOL2 format, chain TB [auth R] MOL2 format, chain V [auth M] MOL2 format, chain W [auth M] MOL2 format, chain WA [auth P] MOL2 format, chain X [auth M] MOL2 format, chain XA [auth P] MOL2 format, chain Y [auth M] MOL2 format, chain YA [auth P] MOL2 format, chain ZA [auth P] mmCIF format, chain AB [auth P] mmCIF format, chain BB [auth P] mmCIF format, chain CB [auth P] mmCIF format, chain DA [auth N] mmCIF format, chain DB [auth P] mmCIF format, chain EA [auth N] mmCIF format, chain FA [auth N] mmCIF format, chain GA [auth N] mmCIF format, chain IB [auth Q] mmCIF format, chain JA [auth C] mmCIF format, chain JB [auth Q] mmCIF format, chain KB [auth Q] mmCIF format, chain LB [auth Q] mmCIF format, chain MA [auth O] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth O] mmCIF format, chain OA [auth O] mmCIF format, chain PA [auth O] mmCIF format, chain QA [auth O] mmCIF format, chain QB [auth R] mmCIF format, chain RA [auth O] mmCIF format, chain RB [auth R] mmCIF format, chain SB [auth R] mmCIF format, chain TB [auth R] mmCIF format, chain V [auth M] mmCIF format, chain W [auth M] mmCIF format, chain WA [auth P] mmCIF format, chain X [auth M] mmCIF format, chain XA [auth P] mmCIF format, chain Y [auth M] mmCIF format, chain YA [auth P] mmCIF format, chain ZA [auth P]	AB [auth P] BB [auth P] CB [auth P] DA [auth N] DB [auth P] AB [auth P], BB [auth P], CB [auth P], DA [auth N], DB [auth P], EA [auth N], FA [auth N], GA [auth N], IB [auth Q], JA [auth C], JB [auth Q], KB [auth Q], LB [auth Q], MA [auth O], N [auth A], NA [auth O], OA [auth O], PA [auth O], QA [auth O], QB [auth R], RA [auth O], RB [auth R], SB [auth R], TB [auth R], V [auth M], W [auth M], WA [auth P], X [auth M], XA [auth P], Y [auth M], YA [auth P], ZA [auth P]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain AB [auth P] Focus chain BB [auth P] Focus chain CB [auth P] Focus chain DA [auth N] Focus chain DB [auth P] Focus chain EA [auth N] Focus chain FA [auth N] Focus chain GA [auth N] Focus chain IB [auth Q] Focus chain JA [auth C] Focus chain JB [auth Q] Focus chain KB [auth Q] Focus chain LB [auth Q] Focus chain MA [auth O] Focus chain N [auth A] Focus chain NA [auth O] Focus chain OA [auth O] Focus chain PA [auth O] Focus chain QA [auth O] Focus chain QB [auth R] Focus chain RA [auth O] Focus chain RB [auth R] Focus chain SB [auth R] Focus chain TB [auth R] Focus chain V [auth M] Focus chain W [auth M] Focus chain WA [auth P] Focus chain X [auth M] Focus chain XA [auth P] Focus chain Y [auth M] Focus chain YA [auth P] Focus chain ZA [auth P] Interactions & Density Focus chain AB [auth P] Focus chain BB [auth P] Focus chain CB [auth P] Focus chain DA [auth N] Focus chain DB [auth P] Focus chain EA [auth N] Focus chain FA [auth N] Focus chain GA [auth N] Focus chain IB [auth Q] Focus chain JA [auth C] Focus chain JB [auth Q] Focus chain KB [auth Q] Focus chain LB [auth Q] Focus chain MA [auth O] Focus chain N [auth A] Focus chain NA [auth O] Focus chain OA [auth O] Focus chain PA [auth O] Focus chain QA [auth O] Focus chain QB [auth R] Focus chain RA [auth O] Focus chain RB [auth R] Focus chain SB [auth R] Focus chain TB [auth R] Focus chain V [auth M] Focus chain W [auth M] Focus chain WA [auth P] Focus chain X [auth M] Focus chain XA [auth P] Focus chain Y [auth M] Focus chain YA [auth P] Focus chain ZA [auth P]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain BA [auth N] SDF format, chain GB [auth Q] SDF format, chain KA [auth O] SDF format, chain OB [auth R] SDF format, chain P [auth M] SDF format, chain UA [auth P] MOL2 format, chain BA [auth N] MOL2 format, chain GB [auth Q] MOL2 format, chain KA [auth O] MOL2 format, chain OB [auth R] MOL2 format, chain P [auth M] MOL2 format, chain UA [auth P] mmCIF format, chain BA [auth N] mmCIF format, chain GB [auth Q] mmCIF format, chain KA [auth O] mmCIF format, chain OB [auth R] mmCIF format, chain P [auth M] mmCIF format, chain UA [auth P]	BA [auth N] GB [auth Q] KA [auth O] OB [auth R] P [auth M] BA [auth N], GB [auth Q], KA [auth O], OB [auth R], P [auth M], UA [auth P]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain BA [auth N] Focus chain GB [auth Q] Focus chain KA [auth O] Focus chain OB [auth R] Focus chain P [auth M] Focus chain UA [auth P] Interactions & Density Focus chain BA [auth N] Focus chain GB [auth Q] Focus chain KA [auth O] Focus chain OB [auth R] Focus chain P [auth M] Focus chain UA [auth P]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain CA [auth N] SDF format, chain HB [auth Q] SDF format, chain LA [auth O] SDF format, chain PB [auth R] SDF format, chain Q [auth M] SDF format, chain R [auth M] SDF format, chain S [auth M] SDF format, chain T [auth M] SDF format, chain VA [auth P] MOL2 format, chain CA [auth N] MOL2 format, chain HB [auth Q] MOL2 format, chain LA [auth O] MOL2 format, chain PB [auth R] MOL2 format, chain Q [auth M] MOL2 format, chain R [auth M] MOL2 format, chain S [auth M] MOL2 format, chain T [auth M] MOL2 format, chain VA [auth P] mmCIF format, chain CA [auth N] mmCIF format, chain HB [auth Q] mmCIF format, chain LA [auth O] mmCIF format, chain PB [auth R] mmCIF format, chain Q [auth M] mmCIF format, chain R [auth M] mmCIF format, chain S [auth M] mmCIF format, chain T [auth M] mmCIF format, chain VA [auth P]	CA [auth N] HB [auth Q] LA [auth O] PB [auth R] Q [auth M] CA [auth N], HB [auth Q], LA [auth O], PB [auth R], Q [auth M], R [auth M], S [auth M], T [auth M], VA [auth P]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth N] Focus chain HB [auth Q] Focus chain LA [auth O] Focus chain PB [auth R] Focus chain Q [auth M] Focus chain R [auth M] Focus chain S [auth M] Focus chain T [auth M] Focus chain VA [auth P] Interactions & Density Focus chain CA [auth N] Focus chain HB [auth Q] Focus chain LA [auth O] Focus chain PB [auth R] Focus chain Q [auth M] Focus chain R [auth M] Focus chain S [auth M] Focus chain T [auth M] Focus chain VA [auth P]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.173 (Depositor), 0.178 (DCC)
R-Value Work: 0.148 (Depositor), 0.153 (DCC)
R-Value Observed: 0.150 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 190.31	α = 90
b = 168.04	β = 132.3
c = 128.16	γ = 90

Software Package:

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