2XDR | pdb_00002xdr

CRYSTALLOGRAPHIC STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE MUTANT E252A FROM PSEUDOMONAS AERUGINOSA

PDB DOI: https://doi.org/10.2210/pdb2XDR/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-05-06 Released: 2011-06-22
Deposition Author(s): Diaz-Sanchez, A.G., Gonzalez-Segura, L., Rudino-Pinera, E., Lira-Rocha, A., Munoz-Clares, R.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.200 (Depositor), 0.194 (DCC)
R-Value Work:
0.160 (Depositor), 0.153 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A Novel Cysteine-Nadph Covalent Adduct in Pseudomonas Aeruginosa Betaine Aldehyde Dehydrogenase Suggests Important Roles for the Reduced Nucleotide in the Reaction Mechanism

Diaz-Sanchez, A.G., Gonzalez-Segura, L., Rudino-Pinera, E., Lira-Rocha, A., Munoz-Clares, R.A.

To be published.

Macromolecule Content

Total Structure Weight: 217.55 kDa
Atom Count: 17,057
Modeled Residue Count: 1,956
Deposited Residue Count: 1,956
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETAINE ALDEHYDE DEHYDROGENASE	A, B, C, D	489	Pseudomonas aeruginosa	Mutation(s): 1 EC: 1.2.1.8
UniProt
Find proteins for Q9HTJ1 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HTJ1 Go to UniProtKB: Q9HTJ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HTJ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain I [auth A] SDF format, chain X [auth C] SDF format, chain P [auth B] MOL2 format, chain EA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain X [auth C] MOL2 format, chain P [auth B] mmCIF format, chain EA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain X [auth C] mmCIF format, chain P [auth B]	EA [auth D], I [auth A], P [auth B], X [auth C]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain EA [auth D] Focus chain I [auth A] Focus chain P [auth B] Focus chain X [auth C] Interactions & Density Focus chain EA [auth D] Focus chain I [auth A] Focus chain P [auth B] Focus chain X [auth C]
TOE Query on TOE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL C₇ H₁₆ O₄ JLGLQAWTXXGVEM-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain J [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain T [auth C] SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain U [auth C] SDF format, chain S [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain J [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain U [auth C] MOL2 format, chain S [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain J [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain T [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain U [auth C] mmCIF format, chain S [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	AA [auth D] BA [auth D] E [auth A] J [auth B] K [auth B] AA [auth D], BA [auth D], E [auth A], J [auth B], K [auth B], L [auth B], M [auth B], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth C], Y [auth D], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain DA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain DA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain DA [auth D]	CA [auth D] DA [auth D] G [auth A] H [auth A] N [auth B] CA [auth D], DA [auth D], G [auth A], H [auth A], N [auth B], O [auth B], V [auth C], W [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain V [auth C] Focus chain W [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.200 (Depositor), 0.194 (DCC)
R-Value Work: 0.160 (Depositor), 0.153 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.555	α = 90
b = 151.555	β = 90
c = 242.406	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-06-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-06-22
Type: Initial release
Version 1.1: 2016-12-14
Changes: Structure summary, Version format compliance
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description