3N9T

Cryatal structure of Hydroxyquinol 1,2-dioxygenase from Pseudomonas putida DLL-E4

PDB DOI: https://doi.org/10.2210/pdb3N9T/pdb

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

Deposited: 2010-05-31 Released: 2010-08-04
Deposition Author(s): Liu, W., Shen, W., Fang, P., Li, J., Cui, Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.244
R-Value Work: 0.184
R-Value Observed: 0.187

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Cryatal structure of Hydroxyquinol 1,2-dioxygenase from Pseudomonas putida DLL-E4

Liu, W., Shen, W., Fang, P., Li, J., Cui, Z.

To be published.

Macromolecule Content

Total Structure Weight: 33.44 kDa
Atom Count: 2,418
Modelled Residue Count: 286
Deposited Residue Count: 290
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PnpC	A	290	Pseudomonas putida	Mutation(s): 0 Gene Names: pnpC EC: 1.13.11.37
UniProt
Find proteins for C6FI44 (Pseudomonas putida) Explore C6FI44 Go to UniProtKB: C6FI44
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C6FI44
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HGX Query on HGX Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	1-HEPTADECANOYL-2-TRIDECANOYL-3-GLYCEROL-PHOSPHONYL CHOLINE C₃₈ H₇₇ N O₈ P AZEAMUNCULVBPK-PSXMRANNSA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.244
R-Value Work: 0.184
R-Value Observed: 0.187
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.362	α = 90
b = 38.933	β = 118.35
c = 82.476	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-08-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-08-04
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: 2018-01-24
Changes: Experimental preparation
Version 1.4: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3N9T

Cryatal structure of Hydroxyquinol 1,2-dioxygenase from Pseudomonas putida DLL-E4

Cryatal structure of Hydroxyquinol 1,2-dioxygenase from Pseudomonas putida DLL-E4

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)