5VBF | pdb_00005vbf

Crystal structure of succinate semialdehyde dehydrogenase from Burkholderia vietnamiensis

PDB DOI: https://doi.org/10.2210/pdb5VBF/pdb

Classification: OXIDOREDUCTASE
Organism(s): Burkholderia vietnamiensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-03-29 Released: 2017-04-12
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.196 (Depositor), 0.196 (DCC)
R-Value Work:
0.147 (Depositor), 0.148 (DCC)
R-Value Observed:
0.148 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5VBF

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

Literature

Crystal structure of succinate semialdehyde dehydrogenase from Burkholderia vietnamiensis

Conrady, D.G., Fox III, D., Lorimer, D.D., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 413.46 kDa
Atom Count: 31,891
Modeled Residue Count: 3,815
Deposited Residue Count: 3,824
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent succinate-semialdehyde dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	478	Burkholderia vietnamiensis	Mutation(s): 0 Gene Names: WK24_04400 EC: 1.2.1.16
UniProt
Find proteins for A4JQH6 (Burkholderia vietnamiensis (strain G4 / LMG 22486)) Explore A4JQH6 Go to UniProtKB: A4JQH6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4JQH6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain DA [auth G] SDF format, chain Q [auth C] SDF format, chain W [auth E] SDF format, chain T [auth D] SDF format, chain M [auth B] SDF format, chain I [auth A] SDF format, chain GA [auth H] SDF format, chain AA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain Q [auth C] MOL2 format, chain W [auth E] MOL2 format, chain T [auth D] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] MOL2 format, chain GA [auth H] MOL2 format, chain AA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain Q [auth C] mmCIF format, chain W [auth E] mmCIF format, chain T [auth D] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A] mmCIF format, chain GA [auth H] mmCIF format, chain AA [auth F]	AA [auth F] DA [auth G] GA [auth H] I [auth A] M [auth B] AA [auth F], DA [auth G], GA [auth H], I [auth A], M [auth B], Q [auth C], T [auth D], W [auth E]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Interactions & Density Focus chain AA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain EA [auth G] SDF format, chain N [auth B] SDF format, chain X [auth E] SDF format, chain U [auth D] SDF format, chain R [auth C] SDF format, chain J [auth A] SDF format, chain HA [auth H] SDF format, chain BA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain N [auth B] MOL2 format, chain X [auth E] MOL2 format, chain U [auth D] MOL2 format, chain R [auth C] MOL2 format, chain J [auth A] MOL2 format, chain HA [auth H] MOL2 format, chain BA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain N [auth B] mmCIF format, chain X [auth E] mmCIF format, chain U [auth D] mmCIF format, chain R [auth C] mmCIF format, chain J [auth A] mmCIF format, chain HA [auth H] mmCIF format, chain BA [auth F]	BA [auth F] EA [auth G] HA [auth H] J [auth A] N [auth B] BA [auth F], EA [auth G], HA [auth H], J [auth A], N [auth B], R [auth C], U [auth D], X [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain J [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain J [auth A] Focus chain N [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain O [auth B] SDF format, chain K [auth A] SDF format, chain IA [auth H] MOL2 format, chain Y [auth E] MOL2 format, chain O [auth B] MOL2 format, chain K [auth A] MOL2 format, chain IA [auth H] mmCIF format, chain Y [auth E] mmCIF format, chain O [auth B] mmCIF format, chain K [auth A] mmCIF format, chain IA [auth H]	IA [auth H], K [auth A], O [auth B], Y [auth E]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain IA [auth H] Focus chain K [auth A] Focus chain O [auth B] Focus chain Y [auth E] Interactions & Density Focus chain IA [auth H] Focus chain K [auth A] Focus chain O [auth B] Focus chain Y [auth E]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain Z [auth E] SDF format, chain P [auth B] SDF format, chain L [auth A] SDF format, chain JA [auth H] SDF format, chain FA [auth G] SDF format, chain CA [auth F] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Z [auth E] MOL2 format, chain P [auth B] MOL2 format, chain L [auth A] MOL2 format, chain JA [auth H] MOL2 format, chain FA [auth G] MOL2 format, chain CA [auth F] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Z [auth E] mmCIF format, chain P [auth B] mmCIF format, chain L [auth A] mmCIF format, chain JA [auth H] mmCIF format, chain FA [auth G] mmCIF format, chain CA [auth F]	CA [auth F] FA [auth G] JA [auth H] L [auth A] P [auth B] CA [auth F], FA [auth G], JA [auth H], L [auth A], P [auth B], S [auth C], V [auth D], Z [auth E]	UNKNOWN ATOM OR ION X		Interactions Focus chain CA [auth F] Focus chain FA [auth G] Focus chain JA [auth H] Focus chain L [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain FA [auth G] Focus chain JA [auth H] Focus chain L [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.196 (Depositor), 0.196 (DCC)
R-Value Work: 0.147 (Depositor), 0.148 (DCC)
R-Value Observed: 0.148 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.62	α = 90
b = 191.76	β = 90
c = 219.8	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MoRDa	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-04-12

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2017-04-12
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.