6BJP

Apo form of the E124S mutant of betaine aldehyde dehydrogenase from Pseudomonas aeruginosa

PDB DOI: https://doi.org/10.2210/pdb6BJP/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2017-11-06 Released: 2018-11-14
Deposition Author(s): Carrizosa-Carbajal, E.I., Gonzalez-Segura, L., Munoz-Clares, R.A.
Funding Organization(s): PAPIIT

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.204
R-Value Work: 0.164
R-Value Observed: 0.166

wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Structural role of Glu124 of betaine aldehyde dehydrogenase from Pseudomonas aeruginosa

Carrizosa-Carbajal, E.I., Gonzalez-Segura, L., Munoz-Clares, R.A.

To be published.

Macromolecule Content

Total Structure Weight: 214.35 kDa
Atom Count: 15,154
Modelled Residue Count: 1,852
Deposited Residue Count: 1,962
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD/NADP-dependent betaine aldehyde dehydrogenase	A, B	490	Pseudomonas aeruginosa PAO1	Mutation(s): 1 Gene Names: betB, PA5373 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HTJ1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD/NADP-dependent betaine aldehyde dehydrogenase	C, D	490	Pseudomonas aeruginosa PAO1	Mutation(s): 1 Gene Names: betB, PA5373 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HTJ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A]	F [auth A], G [auth A], H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B]	I [auth A] J [auth A] K [auth A] M [auth B] N [auth B] I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain R [auth C] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth D]	E [auth A], L [auth B], R [auth C], S [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain S [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A, B	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.204
R-Value Work: 0.164
R-Value Observed: 0.166
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.224	α = 90
b = 96.543	β = 90
c = 280.876	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-11-14

Deposition Author(s):

Carrizosa-Carbajal, E.I.

Gonzalez-Segura, L.

Munoz-Clares, R.A.

Funding Organization	Location	Grant Number
PAPIIT	Mexico	IN220317

Revision History (Full details and data files)

Version 1.0: 2018-11-14
Type: Initial release
Version 2.0: 2020-06-03
Changes: Atomic model, Author supporting evidence, Data collection
Version 2.1: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 2.2: 2023-11-15
Changes: Data collection

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Help and Resources

6BJP

Apo form of the E124S mutant of betaine aldehyde dehydrogenase from Pseudomonas aeruginosa

Structural role of Glu124 of betaine aldehyde dehydrogenase from Pseudomonas aeruginosa

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2