8U9B | pdb_00008u9b

Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from Klebsiella aerogenes (Apo, P21 Form)

PDB DOI: https://doi.org/10.2210/pdb8U9B/pdb

Classification: OXIDOREDUCTASE
Organism(s): Klebsiella aerogenes KCTC 2190
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-09-18 Released: 2023-09-27
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, 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: 1.90 Å
R-Value Free:
0.175 (Depositor), 0.182 (DCC)
R-Value Work:
0.147 (Depositor), 0.157 (DCC)
R-Value Observed:
0.148 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of Betaine aldehyde dehydrogenase (BetB) from Klebsiella aerogenes (Apo, P21 Form)

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

To be published.

Macromolecule Content

Total Structure Weight: 437.79 kDa
Atom Count: 33,696
Modeled Residue Count: 3,923
Deposited Residue Count: 3,992
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, E A, B, C, D, E, F, G, H	499	Klebsiella aerogenes KCTC 2190	Mutation(s): 2 Gene Names: betB_3 EC: 1.2.1.8
UniProt
Find proteins for A0A0H3FPU4 (Klebsiella aerogenes (strain ATCC 13048 / DSM 30053 / CCUG 1429 / JCM 1235 / KCTC 2190 / NBRC 13534 / NCIMB 10102 / NCTC 10006 / CDC 819-56)) Explore A0A0H3FPU4 Go to UniProtKB: A0A0H3FPU4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3FPU4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
B3P Query on B3P Download:Ideal Coordinates CCD File SDF format, chain FA [auth E] SDF format, chain GA [auth E] SDF format, chain OA [auth F] SDF format, chain P [auth B] SDF format, chain U [auth C] MOL2 format, chain FA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain OA [auth F] MOL2 format, chain P [auth B] MOL2 format, chain U [auth C] mmCIF format, chain FA [auth E] mmCIF format, chain GA [auth E] mmCIF format, chain OA [auth F] mmCIF format, chain P [auth B] mmCIF format, chain U [auth C]	FA [auth E], GA [auth E], OA [auth F], P [auth B], U [auth C]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₁₁ H₂₆ N₂ O₆ HHKZCCWKTZRCCL-UHFFFAOYSA-N		Interactions Focus chain FA [auth E] Focus chain GA [auth E] Focus chain OA [auth F] Focus chain P [auth B] Focus chain U [auth C] Interactions & Density Focus chain FA [auth E] Focus chain GA [auth E] Focus chain OA [auth F] Focus chain P [auth B] Focus chain U [auth C]
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain KA [auth E] MOL2 format, chain KA [auth E] mmCIF format, chain KA [auth E]	KA [auth E]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain KA [auth E] Interactions & Density Focus chain KA [auth E]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain J [auth A] SDF format, chain MA [auth F] SDF format, chain N [auth B] SDF format, chain S [auth C] SDF format, chain TA [auth G] SDF format, chain Y [auth D] SDF format, chain YA [auth H] MOL2 format, chain DA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] MOL2 format, chain TA [auth G] MOL2 format, chain Y [auth D] MOL2 format, chain YA [auth H] mmCIF format, chain DA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C] mmCIF format, chain TA [auth G] mmCIF format, chain Y [auth D] mmCIF format, chain YA [auth H]	DA [auth E] J [auth A] MA [auth F] N [auth B] S [auth C] DA [auth E], J [auth A], MA [auth F], N [auth B], S [auth C], TA [auth G], Y [auth D], YA [auth H]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain J [auth A] Focus chain MA [auth F] Focus chain N [auth B] Focus chain S [auth C] Focus chain TA [auth G] Focus chain Y [auth D] Focus chain YA [auth H] Interactions & Density Focus chain DA [auth E] Focus chain J [auth A] Focus chain MA [auth F] Focus chain N [auth B] Focus chain S [auth C] Focus chain TA [auth G] Focus chain Y [auth D] Focus chain YA [auth H]
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain W [auth C] MOL2 format, chain W [auth C] mmCIF format, chain W [auth C]	W [auth C]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain W [auth C] Interactions & Density Focus chain W [auth C]
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain AB [auth H] SDF format, chain BA [auth D] SDF format, chain IA [auth E] SDF format, chain JA [auth E] SDF format, chain L [auth A] SDF format, chain PA [auth F] SDF format, chain Q [auth B] SDF format, chain QA [auth F] SDF format, chain RA [auth F] SDF format, chain V [auth C] SDF format, chain VA [auth G] SDF format, chain WA [auth G] SDF format, chain HA [auth E] MOL2 format, chain AA [auth D] MOL2 format, chain AB [auth H] MOL2 format, chain BA [auth D] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain PA [auth F] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain RA [auth F] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth G] MOL2 format, chain WA [auth G] MOL2 format, chain HA [auth E] mmCIF format, chain AA [auth D] mmCIF format, chain AB [auth H] mmCIF format, chain BA [auth D] mmCIF format, chain IA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain PA [auth F] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain RA [auth F] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth G] mmCIF format, chain WA [auth G] mmCIF format, chain HA [auth E]	AA [auth D] AB [auth H] BA [auth D] HA [auth E] IA [auth E] AA [auth D], AB [auth H], BA [auth D], HA [auth E], IA [auth E], JA [auth E], L [auth A], PA [auth F], Q [auth B], QA [auth F], RA [auth F], V [auth C], VA [auth G], WA [auth G]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain AB [auth H] Focus chain BA [auth D] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain L [auth A] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain V [auth C] Focus chain VA [auth G] Focus chain WA [auth G] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth H] Focus chain BA [auth D] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain L [auth A] Focus chain PA [auth F] Focus chain Q [auth B] Focus chain QA [auth F] Focus chain RA [auth F] Focus chain V [auth C] Focus chain VA [auth G] Focus chain WA [auth G]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain EA [auth E] SDF format, chain K [auth A] SDF format, chain NA [auth F] SDF format, chain O [auth B] SDF format, chain T [auth C] SDF format, chain Z [auth D] SDF format, chain ZA [auth H] SDF format, chain UA [auth G] MOL2 format, chain EA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain ZA [auth H] MOL2 format, chain UA [auth G] mmCIF format, chain EA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain T [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain ZA [auth H] mmCIF format, chain UA [auth G]	EA [auth E] K [auth A] NA [auth F] O [auth B] T [auth C] EA [auth E], K [auth A], NA [auth F], O [auth B], T [auth C], UA [auth G], Z [auth D], ZA [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain EA [auth E] Focus chain K [auth A] Focus chain NA [auth F] Focus chain O [auth B] Focus chain T [auth C] Focus chain UA [auth G] Focus chain Z [auth D] Focus chain ZA [auth H] Interactions & Density Focus chain EA [auth E] Focus chain K [auth A] Focus chain NA [auth F] Focus chain O [auth B] Focus chain T [auth C] Focus chain UA [auth G] Focus chain Z [auth D] Focus chain ZA [auth H]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain I [auth A] SDF format, chain LA [auth F] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain SA [auth G] SDF format, chain X [auth D] SDF format, chain XA [auth H] MOL2 format, chain CA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain SA [auth G] MOL2 format, chain X [auth D] MOL2 format, chain XA [auth H] mmCIF format, chain CA [auth E] mmCIF format, chain I [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain SA [auth G] mmCIF format, chain X [auth D] mmCIF format, chain XA [auth H]	CA [auth E] I [auth A] LA [auth F] M [auth B] R [auth C] CA [auth E], I [auth A], LA [auth F], M [auth B], R [auth C], SA [auth G], X [auth D], XA [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain I [auth A] Focus chain LA [auth F] Focus chain M [auth B] Focus chain R [auth C] Focus chain SA [auth G] Focus chain X [auth D] Focus chain XA [auth H] Interactions & Density Focus chain CA [auth E] Focus chain I [auth A] Focus chain LA [auth F] Focus chain M [auth B] Focus chain R [auth C] Focus chain SA [auth G] Focus chain X [auth D] Focus chain XA [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.175 (Depositor), 0.182 (DCC)
R-Value Work: 0.147 (Depositor), 0.157 (DCC)
R-Value Observed: 0.148 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.27	α = 90
b = 161.235	β = 101.11
c = 158.708	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-09-27

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease

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	75N93022C00036
National Institutes of Health/Office of the Director	United States	S10OD030394