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- PDB-7bu3: Structure of alcohol dehydrogenase YjgB in complex with NADP from... -

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Basic information

Entry
Database: PDB / ID: 7bu3
TitleStructure of alcohol dehydrogenase YjgB in complex with NADP from Escherichia coli
Components(Alcohol dehydrogenase) x 2
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
ASPARTIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / alcohol dehydrogenase (NADP(+)) / Aldehyde reductase Ahr / Aldehyde reductase Ahr
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 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 1.1Dec 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 1.2Nov 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)74,76213
Polymers72,4842
Non-polymers2,27811
Water10,647591
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)64.970, 138.990, 168.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Alcohol dehydrogenase / Aldehyde reductase Ahr / NADPH-dependent aldehyde reductase Ahr


Mass: 36146.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SF file contains Friedel pairs. / Source: (gene. exp.) Escherichia coli (E. coli)
Gene: ahr, AWG90_000500, B9M99_17975, B9T59_09540, C6B13_12130, CDC27_23140, D2188_25420, D3P01_20900, D9G11_20970, D9I87_13335, DND16_13855, DNQ45_13310, DU321_18055, E0L12_15935, ECONIH1_25310, ...Gene: ahr, AWG90_000500, B9M99_17975, B9T59_09540, C6B13_12130, CDC27_23140, D2188_25420, D3P01_20900, D9G11_20970, D9I87_13335, DND16_13855, DNQ45_13310, DU321_18055, E0L12_15935, ECONIH1_25310, ELV08_20515, EQ830_17095, EXX23_18790, EXX53_16635, FNJ83_00500, FV293_01340, MS6198_49940
Production host: Escherichia coli (E. coli)
References: UniProt: A0A094VUC2, UniProt: P27250*PLUS, alcohol dehydrogenase (NADP+)
#2: 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: 36337.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: yjgB, ahr, A9P13_23120, A9X72_22295, AC789_1c46870, AM446_24685, AM464_15880, AUQ13_10955, AWP75_26740, BE963_12920, BON76_03580, BON87_21450, BvCms2454_04261, BvCmsKKP061_04826, BvCmsKSP011_ ...Gene: yjgB, ahr, A9P13_23120, A9X72_22295, 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, DU309_23350, EC3234A_79c00790, ERS085365_04790, ERS085374_04180, ERS085416_04717, ERS139211_04850, EYY27_20520, 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+)

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Non-polymers , 6 types, 602 molecules

#3: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#4: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 591 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl, pH 7.0, 16% (w/v) PEG 3350 , 0.2 M Lithium Sulfate, 5 mM NADPH

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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 315r / Detector: CCD / Date: Dec 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.45→29.55 Å / Num. obs: 134685 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.998 / Net I/σ(I): 8.07
Reflection shellResolution: 1.45→1.49 Å / Num. unique obs: 9859 / CC1/2: 0.038

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Processing

Software
NameVersionClassification
PHENIX(1.18_3845: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7BU2

7bu2


Resolution: 2→29.55 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1995 3829 3.84 %
Rwork0.1601 --
obs0.1616 99594 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5084 0 134 591 5809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085324
X-RAY DIFFRACTIONf_angle_d0.9037235
X-RAY DIFFRACTIONf_dihedral_angle_d16.005772
X-RAY DIFFRACTIONf_chiral_restr0.056808
X-RAY DIFFRACTIONf_plane_restr0.005926
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.30571430.22823581X-RAY DIFFRACTION100
2.03-2.050.27631390.20573515X-RAY DIFFRACTION100
2.05-2.080.28311410.20773577X-RAY DIFFRACTION100
2.08-2.110.27951420.20343523X-RAY DIFFRACTION100
2.11-2.140.28281420.19563548X-RAY DIFFRACTION100
2.14-2.170.25511440.18143586X-RAY DIFFRACTION100
2.17-2.210.19741420.18193491X-RAY DIFFRACTION100
2.21-2.250.20871460.18533563X-RAY DIFFRACTION100
2.25-2.290.21731440.18793521X-RAY DIFFRACTION100
2.29-2.330.22071410.17473534X-RAY DIFFRACTION100
2.33-2.380.2551450.17923538X-RAY DIFFRACTION100
2.38-2.430.24621430.17383555X-RAY DIFFRACTION100
2.43-2.490.22251430.17773575X-RAY DIFFRACTION100
2.49-2.550.19221400.17563538X-RAY DIFFRACTION100
2.55-2.620.22671410.17863542X-RAY DIFFRACTION100
2.62-2.70.25411420.16573519X-RAY DIFFRACTION100
2.7-2.780.19841370.17183570X-RAY DIFFRACTION100
2.78-2.880.22331450.16393540X-RAY DIFFRACTION100
2.88-30.23381410.16273549X-RAY DIFFRACTION100
3-3.140.16231400.15633558X-RAY DIFFRACTION100
3.14-3.30.19841400.15293546X-RAY DIFFRACTION100
3.3-3.510.17571380.14453548X-RAY DIFFRACTION100
3.51-3.780.1831440.14213544X-RAY DIFFRACTION100
3.78-4.160.151420.13353524X-RAY DIFFRACTION100
4.16-4.760.13611440.123590X-RAY DIFFRACTION100
4.76-5.980.18581390.15123540X-RAY DIFFRACTION100
5.98-29.550.1831410.14983550X-RAY DIFFRACTION100

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