6BPG | pdb_00006bpg

Crystal structure of betaine aldehyde dehydrogenase from Pseudomonas aeruginosa with bound rubidium ions

PDB DOI: https://doi.org/10.2210/pdb6BPG/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-11-23 Released: 2018-11-28
Deposition Author(s): Lopez-Orduna, E.F., Munoz-Clares, R.A., Gonzalez-Segura, L.
Funding Organization(s): Consejo Nacional de Ciencia y Tecnologia (CONACYT)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.09 Å
R-Value Free:
0.234 (Depositor), 0.230 (DCC)
R-Value Work:
0.181 (Depositor), 0.180 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystallographic identification of monovalent cation-binding sites in two betaine aldehyde dehydrogenases

Lopez-Orduna, E.F., Munoz-Clares, R.A., Gonzalez-Segura, L.

To be published.

Macromolecule Content

Total Structure Weight: 428.49 kDa
Atom Count: 29,968
Modeled Residue Count: 3,912
Deposited Residue Count: 3,920
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD/NADP-dependent betaine aldehyde dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	490	Pseudomonas aeruginosa PAO1	Mutation(s): 0 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RB Query on RB Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain U [auth G] SDF format, chain X [auth H] SDF format, chain W [auth G] SDF format, chain V [auth G] SDF format, chain T [auth F] SDF format, chain S [auth F] SDF format, chain R [auth E] SDF format, chain Q [auth E] SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain K [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain U [auth G] MOL2 format, chain X [auth H] MOL2 format, chain W [auth G] MOL2 format, chain V [auth G] MOL2 format, chain T [auth F] MOL2 format, chain S [auth F] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain U [auth G] mmCIF format, chain X [auth H] mmCIF format, chain W [auth G] mmCIF format, chain V [auth G] mmCIF format, chain T [auth F] mmCIF format, chain S [auth F] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth E] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] K [auth B] L [auth B] M [auth C] I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth C], O [auth D], P [auth D], Q [auth E], R [auth E], S [auth F], T [auth F], U [auth G], V [auth G], W [auth G], X [auth H]	RUBIDIUM ION Rb NCCSSGKUIKYAJD-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.09 Å
R-Value Free: 0.234 (Depositor), 0.230 (DCC)
R-Value Work: 0.181 (Depositor), 0.180 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 325.954	α = 90
b = 130.358	β = 94.93
c = 100.695	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: 2018-11-28

Deposition Author(s):

Lopez-Orduna, E.F.

Munoz-Clares, R.A.

Gonzalez-Segura, L.

Funding Organization	Location	Grant Number
Consejo Nacional de Ciencia y Tecnologia (CONACYT)	Mexico	101986

Revision History (Full details and data files)

Version 1.0: 2018-11-28
Type: Initial release
Version 1.1: 2020-01-08
Changes: Author supporting evidence
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description