3MEQ | pdb_00003meq

Crystal structure of alcohol dehydrogenase from Brucella melitensis

PDB DOI: https://doi.org/10.2210/pdb3MEQ/pdb

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

Deposited: 2010-03-31 Released: 2010-04-28
Deposition Author(s): Arakaki, T.L., Staker, B.L., Gardberg, A., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.204 (Depositor), 0.199 (DCC)
R-Value Work:
0.171 (Depositor)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of alcohol dehydrogenase from Brucella melitensis

Arakaki, T.L., Gardberg, A., Staker, B.L., Sankaran, B.

To be published.

Macromolecule Content

Total Structure Weight: 156.63 kDa
Atom Count: 10,753
Modeled Residue Count: 1,351
Deposited Residue Count: 1,460
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alcohol dehydrogenase, zinc-containing	A, B, C, D	365	Brucella suis	Mutation(s): 0 Gene Names: BR0203 EC: 1.1.1.1
UniProt
Find proteins for A0A0H3G9R2 (Brucella suis biovar 1 (strain 1330)) Explore A0A0H3G9R2 Go to UniProtKB: A0A0H3G9R2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3G9R2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI Query on NAI Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain V [auth C] SDF format, chain N [auth B] SDF format, chain L [auth B] SDF format, chain G [auth A] SDF format, chain E [auth A] SDF format, chain DA [auth D] SDF format, chain BA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain V [auth C] MOL2 format, chain N [auth B] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth D] MOL2 format, chain BA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain V [auth C] mmCIF format, chain N [auth B] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth D] mmCIF format, chain BA [auth D]	BA [auth D] DA [auth D] E [auth A] G [auth A] L [auth B] BA [auth D], DA [auth D], E [auth A], G [auth A], L [auth B], N [auth B], V [auth C], X [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain N [auth B] Focus chain V [auth C] Focus chain X [auth C] Interactions & Density Focus chain BA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain N [auth B] Focus chain V [auth C] Focus chain X [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain W [auth C] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain I [auth A] SDF format, chain GA [auth D] SDF format, chain FA [auth D] SDF format, chain F [auth A] SDF format, chain EA [auth D] SDF format, chain CA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain W [auth C] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain CA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain W [auth C] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain GA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain CA [auth D]	CA [auth D] EA [auth D] F [auth A] FA [auth D] GA [auth D] CA [auth D], EA [auth D], F [auth A], FA [auth D], GA [auth D], I [auth A], K [auth A], M [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], W [auth C], Z [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain I [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain W [auth C] Focus chain Z [auth C] Interactions & Density Focus chain CA [auth D] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain I [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain W [auth C] Focus chain Z [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain J [auth A] MOL2 format, chain Y [auth C] MOL2 format, chain J [auth A] mmCIF format, chain Y [auth C] mmCIF format, chain J [auth A]	J [auth A], Y [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain Y [auth C] Interactions & Density Focus chain J [auth A] Focus chain Y [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain AA [auth C]	AA [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Interactions & Density Focus chain AA [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.204 (Depositor), 0.199 (DCC)
R-Value Work: 0.171 (Depositor)
R-Value Observed: 0.173 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.365	α = 90
b = 103.799	β = 90
c = 152.39	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-04-28

Deposition Author(s):

Arakaki, T.L.

Staker, B.L.

Gardberg, A.

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2010-04-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description