3TH1 | pdb_00003th1

Crystal structure of chlorocatechol 1,2-dioxygenase from Pseudomonas putida

PDB DOI: https://doi.org/10.2210/pdb3TH1/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas putida
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-08-18 Released: 2012-08-22
Deposition Author(s): Rustiguel, J.K., Nonato, M.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free:
0.279 (Depositor), 0.280 (DCC)
R-Value Work:
0.227 (Depositor), 0.220 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of chlorocatechol 1,2-dioxygenase from Pseudomonas putida

Rustiguel, J.K., Barbosa, L.R.S., Araujo, A.P.U., Nonato, M.C.

To be published.

Macromolecule Content

Total Structure Weight: 89.25 kDa
Atom Count: 5,462
Modeled Residue Count: 727
Deposited Residue Count: 780
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorocatechol 1,2-dioxygenase	A, B, C	260	Pseudomonas putida	Mutation(s): 0 Gene Names: clcA EC: 1.13.11
UniProt
Find proteins for P11451 (Pseudomonas putida) Explore P11451 Go to UniProtKB: P11451
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11451
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3PH Query on 3PH Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B]	F [auth A], M [auth B]	1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE C₃₉ H₇₇ O₈ P YFWHNAWEOZTIPI-DIPNUNPCSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]
DTD Query on DTD Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B]	E [auth A], L [auth B]	DITHIANE DIOL C₄ H₈ O₂ S₂ YPGMOWHXEQDBBV-IMJSIDKUSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain N [auth B] MOL2 format, chain J [auth B] MOL2 format, chain N [auth B] mmCIF format, chain J [auth B] mmCIF format, chain N [auth B]	J [auth B], N [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain N [auth B] Interactions & Density Focus chain J [auth B] Focus chain N [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C]	D [auth A], K [auth B], O [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Focus chain O [auth C] Interactions & Density Focus chain D [auth A] Focus chain K [auth B] Focus chain O [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.40 Å
R-Value Free: 0.279 (Depositor), 0.280 (DCC)
R-Value Work: 0.227 (Depositor), 0.220 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.57	α = 90
b = 97.57	β = 90
c = 423.6	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-08-22

Deposition Author(s):

Rustiguel, J.K.

Nonato, M.C.

Revision History (Full details and data files)

Version 1.0: 2012-08-22
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