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

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.3 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] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF 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 P [auth B] SDF format, chain O [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 P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF 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] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain R [auth C] mmCIF 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
Version 2.3: 2024-10-09
Changes: Structure summary

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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