2BUU | pdb_00002buu

Crystal Structure Of Protocatechuate 3,4-Dioxygenase from Acinetobacter Sp. ADP1 Mutant R457S in complex with 4-Nitrocatechol

PDB DOI: https://doi.org/10.2210/pdb2BUU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Acinetobacter baylyi ADP1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-06-17 Released: 2006-10-26
Deposition Author(s): Vetting, M.W., Valley, M.P., D'Argenio, D.A., Ornston, L.N., Lipscomb, J.D., Ohlendorf, D.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.201 (Depositor), 0.199 (DCC)
R-Value Work:
0.167 (Depositor), 0.166 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystallographic Studies of Intradiol Dioxygenases.

Vetting, M.W.

(2001) Phd Thesis

Macromolecule Content

Total Structure Weight: 51.23 kDa
Atom Count: 3,774
Modeled Residue Count: 440
Deposited Residue Count: 450
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHAIN	A	209	Acinetobacter baylyi ADP1	Mutation(s): 0 EC: 1.13.11.3
UniProt
Find proteins for P20371 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)) Explore P20371 Go to UniProtKB: P20371
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20371
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAIN	B	241	Acinetobacter baylyi ADP1	Mutation(s): 1 EC: 1.13.11.3
UniProt
Find proteins for P20372 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)) Explore P20372 Go to UniProtKB: P20372
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20372
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4NC Query on 4NC Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	4-NITROCATECHOL C₆ H₅ N O₄ XJNPNXSISMKQEX-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.201 (Depositor), 0.199 (DCC)
R-Value Work: 0.167 (Depositor), 0.166 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.58	α = 90
b = 144.58	β = 90
c = 144.58	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-10-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-10-26
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-05-22
Changes: Data collection, Other, Refinement description
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description