3EK1 | pdb_00003ek1

Crystal structure of aldehyde dehydrogenase from brucella melitensis biovar abortus 2308

PDB DOI: https://doi.org/10.2210/pdb3EK1/pdb

Classification: OXIDOREDUCTASE
Organism(s): Brucella abortus 2308
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-09-18 Released: 2008-09-30
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.225 (Depositor), 0.220 (DCC)
R-Value Work:
0.161 (Depositor), 0.160 (DCC)
R-Value Observed:
0.164 (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

Crystal structure of aldehyde dehydrogenase from brucella melitensis biovar abortus 2308

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Macromolecule Content

Total Structure Weight: 431.24 kDa
Atom Count: 32,199
Modeled Residue Count: 3,865
Deposited Residue Count: 4,032
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aldehyde dehydrogenase	A, B, C, D, E A, B, C, D, E, F, G, H	504	Brucella abortus 2308	Mutation(s): 0 Gene Names: gabD, BAB1_1655 EC: 1.2.1.16
UniProt
Find proteins for Q2YRI3 (Brucella abortus (strain 2308)) Explore Q2YRI3 Go to UniProtKB: Q2YRI3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2YRI3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain X [auth H] SDF format, chain V [auth G] SDF format, chain T [auth F] SDF format, chain R [auth E] SDF format, chain P [auth D] SDF format, chain L [auth B] SDF format, chain J [auth A] MOL2 format, chain N [auth C] MOL2 format, chain X [auth H] MOL2 format, chain V [auth G] MOL2 format, chain T [auth F] MOL2 format, chain R [auth E] MOL2 format, chain P [auth D] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] mmCIF format, chain N [auth C] mmCIF format, chain X [auth H] mmCIF format, chain V [auth G] mmCIF format, chain T [auth F] mmCIF format, chain R [auth E] mmCIF format, chain P [auth D] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A]	J [auth A] L [auth B] N [auth C] P [auth D] R [auth E] J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth F], V [auth G], X [auth H]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain W [auth H] SDF format, chain U [auth G] SDF format, chain S [auth F] SDF format, chain Q [auth E] SDF format, chain K [auth B] SDF format, chain I [auth A] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain W [auth H] MOL2 format, chain U [auth G] MOL2 format, chain S [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain W [auth H] mmCIF format, chain U [auth G] mmCIF format, chain S [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A]	I [auth A] K [auth B] M [auth C] O [auth D] Q [auth E] I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], U [auth G], W [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.225 (Depositor), 0.220 (DCC)
R-Value Work: 0.161 (Depositor), 0.160 (DCC)
R-Value Observed: 0.164 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33EK1

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.87	α = 92.03
b = 93.01	β = 107.58
c = 143.7	γ = 109.65

Software Package:

Software Name	Purpose
BOS	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2008-09-30

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2008-09-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description