3VB0 | pdb_00003vb0

Crystal structure of 2,2',3-trihydroxybiphenyl 1,2-dioxygenase from dibenzofuran-degrading Sphingomonas wittichii strain RW1

PDB DOI: https://doi.org/10.2210/pdb3VB0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhizorhabdus wittichii RW1
Expression System: Pseudomonas putida
Mutation(s): No

Deposited: 2011-12-30 Released: 2013-04-03
Deposition Author(s): Koksal, M., Kumar, P., Bolin, J.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.289 (Depositor), 0.290 (DCC)
R-Value Work:
0.254 (Depositor), 0.250 (DCC)
R-Value Observed:
0.256 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a dibenzofuran-degrading dioxygenase: an unusual spatially heterogeneous crystal with a hypersymmetric intensity distribution

Koksal, M., Kumar, P., Fortin, P.D., Eltis, L.D., Bolin, J.T.

To be published.

Macromolecule Content

Total Structure Weight: 130.23 kDa
Atom Count: 9,162
Modeled Residue Count: 1,156
Deposited Residue Count: 1,176
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase/bleomycin resistance protein/dioxygenase	A, B, C, D	294	Rhizorhabdus wittichii RW1	Mutation(s): 0 Gene Names: dbfB, Swit_4902 EC: 1.13.11
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	F [auth A], I [auth B]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B]	G [auth A], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth B]
FE2 Query on FE2 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D]	E [auth A], H [auth B], K [auth C], L [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.289 (Depositor), 0.290 (DCC)
R-Value Work: 0.254 (Depositor), 0.250 (DCC)
R-Value Observed: 0.256 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.587	α = 90
b = 131.587	β = 90
c = 103.146	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-04-03

Deposition Author(s):

Koksal, M.

Kumar, P.

Bolin, J.T.

Revision History (Full details and data files)

Version 1.0: 2013-04-03
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-04-03
Changes: Refinement description