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- PDB-7utw: Cd-substituted Horse Liver Alcohol Dehydrogenase in Complex with ... -

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Basic information

Entry
Database: PDB / ID: 7utw
TitleCd-substituted Horse Liver Alcohol Dehydrogenase in Complex with NADH and N-Cyclohexylformamide
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / Ternary complex
Function / homology
Function and homology information


all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinoic acid metabolic process / retinol metabolic process / zinc ion binding / cytosol
Similarity search - Function
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 ...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
: / CYCLOHEXYLFORMAMIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsZheng, C. / Boxer, S.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118044 United States
CitationJournal: Nat.Chem. / Year: 2023
Title: Enhanced active-site electric field accelerates enzyme catalysis.
Authors: Zheng, C. / Ji, Z. / Mathews, I.I. / Boxer, S.G.
History
DepositionApr 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 6, 2023Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 13, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)82,01810
Polymers80,0772
Non-polymers1,9418
Water19,5641086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-49 kcal/mol
Surface area26440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.206, 50.807, 92.903
Angle α, β, γ (deg.)92.390, 102.930, 109.330
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alcohol dehydrogenase E chain


Mass: 40038.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: horse liver protein / Source: (gene. exp.) Equus caballus (horse) / Production host: Escherichia coli (E. coli) / References: UniProt: P00327, alcohol dehydrogenase

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Non-polymers , 5 types, 1094 molecules

#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#5: Chemical ChemComp-CXF / CYCLOHEXYLFORMAMIDE


Mass: 127.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H13NO / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1086 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: PEG400(10%-25%), 2mM NADH, 10mM N-cyclohexylformamide in Tris buffer at pH 8.20

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.33→38.02 Å / Num. obs: 150446 / % possible obs: 88.5 % / Redundancy: 7.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.027 / Rrim(I) all: 0.076 / Net I/σ(I): 16.1 / Num. measured all: 1155326 / Scaling rejects: 1479
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.33-1.357.21.0355072670250.8280.4061.1132.283.4
7.28-38.027.90.03807510190.9990.0110.0325699

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Processing

Software
NameVersionClassification
Aimless0.7.7data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DWV

4dwv


Resolution: 1.33→38.02 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 16.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.165 7516 5 %
Rwork0.1376 142729 -
obs0.139 150245 88.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.34 Å2 / Biso mean: 19.0438 Å2 / Biso min: 8.42 Å2
Refinement stepCycle: final / Resolution: 1.33→38.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 110 1086 6766
Biso mean--13.51 33.27 -
Num. residues----748
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.33-1.340.24852270.22484328455580
1.34-1.360.22492530.19114820507389
1.36-1.380.24972520.20534754500688
1.38-1.390.23382490.18134739498889
1.39-1.410.2252510.17544767501888
1.41-1.430.20622460.16324663490987
1.43-1.450.18912430.16084621486485
1.45-1.470.21612360.16124465470183
1.47-1.50.20382340.15354440467483
1.5-1.520.18342560.134861511791
1.52-1.550.17112560.13074848510490
1.55-1.580.15652540.12064848510290
1.58-1.610.16742520.11524779503190
1.61-1.640.14262550.11464847510289
1.64-1.670.16342470.11724673492088
1.67-1.710.14722460.11644667491386
1.71-1.760.15092260.12294301452780
1.76-1.80.16592590.12774922518192
1.8-1.860.15752600.12814938519892
1.86-1.920.16982580.12654915517391
1.92-1.980.15192560.13024864512091
1.98-2.060.16442560.13254859511590
2.06-2.160.1572470.13424681492887
2.16-2.270.17692390.14074537477684
2.27-2.410.15182670.12845071533894
2.41-2.60.15392630.13994995525893
2.6-2.860.1752560.14724885514191
2.86-3.280.1722440.14944616486086
3.28-4.130.16632690.1385107537695
4.13-38.020.12782590.12664918517791

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