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- PDB-7bu2: Structure of alcohol dehydrogenase YjgB from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 7bu2
TitleStructure of alcohol dehydrogenase YjgB from Escherichia coli
ComponentsAlcohol dehydrogenase
KeywordsOXIDOREDUCTASE / Alcohol Dehydrogenase
Function / homology
Function and homology information


alcohol dehydrogenase (NADP+) / alcohol dehydrogenase (NADP+) activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / fatty acid metabolic process / protein homodimerization activity / zinc ion binding
Similarity search - Function
: / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain ...: / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / alcohol dehydrogenase (NADP(+)) / Aldehyde reductase Ahr
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.553 Å
AuthorsNguyen, G.T. / Kim, Y.-G. / Ahn, J.-W. / Chang, J.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2019R1A2C4069796 Korea, Republic Of
CitationJournal: Molecules / Year: 2020
Title: Structural Basis for Broad Substrate Selectivity of Alcohol Dehydrogenase YjgB from Escherichia coli .
Authors: Nguyen, G.T. / Kim, Y.G. / Ahn, J.W. / Chang, J.H.
History
DepositionApr 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Advisory / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.2Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alcohol dehydrogenase
B: Alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,07614
Polymers75,1382
Non-polymers93812
Water14,232790
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.138, 64.470, 81.663
Angle α, β, γ (deg.)90.000, 106.140, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-808-

HOH

21A-830-

HOH

31B-849-

HOH

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Components

#1: Protein Alcohol dehydrogenase / Aldehyde reductase Ahr / Aldehyde reductase / NADPH-dependent / Zn-containing / broad specificity / ...Aldehyde reductase Ahr / Aldehyde reductase / NADPH-dependent / Zn-containing / broad specificity / NADPH-dependent aldehyde reductase Ahr / Oxidoreductase / YjgB / Zinc-binding dehydrogenase family protein


Mass: 37568.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: yjgB, ahr, AC789_1c46870, AM446_24685, AM464_15880, AUQ13_10955, AWP75_26740, BE963_12920, BON76_03580, BON87_21450, BvCms2454_04261, BvCmsKKP061_04826, BvCmsKSP011_04570, BvCmsKSP024_01161, ...Gene: yjgB, ahr, AC789_1c46870, AM446_24685, AM464_15880, AUQ13_10955, AWP75_26740, BE963_12920, BON76_03580, BON87_21450, BvCms2454_04261, BvCmsKKP061_04826, BvCmsKSP011_04570, BvCmsKSP024_01161, BvCmsKSP045_03147, BvCmsKSP067_02166, BvCmsNSP047_01920, CRX46_16815, D9J60_11645, DJ503_08680, DS732_03420, EC3234A_79c00790, ERS085365_04790, ERS085374_04180, ERS085416_04717, ERS139211_04850, EYY27_20520, F0312_23505, F1E03_04805, FNJ69_20595, NCTC8959_04532, NCTC9050_02355, NCTC9077_05531, NCTC9117_05474, PGD_03453, SAMEA3472056_04737, WR15_06500, YDC107_2991
Production host: Escherichia coli (E. coli)
References: UniProt: A0A024L8S1, UniProt: P27250*PLUS, alcohol dehydrogenase (NADP+)
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 790 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl, pH 7.0, and 16% (w/v) PEG 3350 with 0.2 M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 95566 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.97465 / Net I/σ(I): 36.2
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 4760 / CC1/2: 0.894

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YQD

1yqd


Resolution: 1.553→25.015 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.53
RfactorNum. reflection% reflection
Rfree0.1936 4781 5 %
Rwork0.1607 --
obs0.1623 95547 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.42 Å2 / Biso mean: 23.8661 Å2 / Biso min: 9.71 Å2
Refinement stepCycle: final / Resolution: 1.553→25.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5105 0 54 790 5949
Biso mean--29.31 36.54 -
Num. residues----676
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135436
X-RAY DIFFRACTIONf_angle_d1.47364
X-RAY DIFFRACTIONf_chiral_restr0.061813
X-RAY DIFFRACTIONf_plane_restr0.008970
X-RAY DIFFRACTIONf_dihedral_angle_d13.7351977
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.553-1.57040.25171390.2179278891
1.5704-1.58890.27291590.2212983100
1.5889-1.60830.25911670.21023032100
1.6083-1.62860.20331510.20153017100
1.6286-1.65010.25251640.19783027100
1.6501-1.67270.26151720.19912998100
1.6727-1.69660.23331790.19562985100
1.6966-1.72190.25051650.19723024100
1.7219-1.74880.2351710.19662993100
1.7488-1.77740.20461470.1883040100
1.7774-1.80810.23591710.18423050100
1.8081-1.84090.22591620.1792985100
1.8409-1.87630.22931700.17682996100
1.8763-1.91460.23761540.16893051100
1.9146-1.95620.18361670.16693036100
1.9562-2.00170.22311490.1743041100
2.0017-2.05180.19591520.16923018100
2.0518-2.10720.20661670.16043005100
2.1072-2.16920.2011420.15793056100
2.1692-2.23920.18321550.15453036100
2.2392-2.31910.20051620.16253030100
2.3191-2.41190.20241430.15883044100
2.4119-2.52160.19131730.16343008100
2.5216-2.65440.17761500.15843084100
2.6544-2.82050.16511630.15223040100
2.8205-3.03790.16971490.15783043100
3.0379-3.3430.18071490.14993073100
3.343-3.82530.15871730.13973057100
3.8253-4.81380.1621650.13043063100
4.8138-25.0150.20871510.16133163100

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