8SKF | pdb_00008skf

Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from Klebsiella aerogenes (Lattice Translocation Disorder)

PDB DOI: https://doi.org/10.2210/pdb8SKF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Klebsiella aerogenes
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-04-19 Released: 2023-04-26
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.207 (Depositor), 0.210 (DCC)
R-Value Work:
0.174 (Depositor), 0.180 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from Klebsiella aerogenes (Lattice Translocation Disorder)

Liu, L., Lovell, S., Battaile, K.P., Cooper, A.

To be published.

Macromolecule Content

Total Structure Weight: 110.58 kDa
Atom Count: 8,637
Modelled Residue Count: 986
Deposited Residue Count: 998
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Betaine aldehyde dehydrogenase	A, B	499	Klebsiella aerogenes	Mutation(s): 2 Gene Names: betB_3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD (Subject of Investigation/LOI) Query on NAD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	G [auth A], H [auth A], L [auth B], M [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	C [auth A], E [auth A], J [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain J [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B]	F [auth A], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.207 (Depositor), 0.210 (DCC)
R-Value Work: 0.174 (Depositor), 0.180 (DCC)
R-Value Observed: 0.176 (Depositor)

Diffraction Data: https://doi.org/10.18430/M38SKF

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.822	α = 90
b = 184.823	β = 90
c = 163.066	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-04-26

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700059C
National Institutes of Health/Office of the Director	United States	S10OD030394