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- PDB-7rm6: Horse liver alcohol dehydrogenase in complex with NADH and N-cylc... -

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Basic information

Entry
Database: PDB / ID: 7rm6
TitleHorse liver alcohol dehydrogenase in complex with NADH and N-cylcohexyl formamide
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE/INHIBITOR / Hydride transfer / Zinc metalloenzyme / OXIDOREDUCTASE / OXIDOREDUCTASE-INHIBITOR complex
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / 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 domain superfamily
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: 1.43 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: 2022
Title: A two-directional vibrational probe reveals different electric field orientations in solution and an enzyme active site.
Authors: Zheng, C. / Mao, Y. / Kozuch, J. / Atsango, A.O. / Ji, Z. / Markland, T.E. / Boxer, S.G.
History
DepositionJul 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)81,92410
Polymers80,0772
Non-polymers1,8478
Water13,998777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.142, 50.979, 92.864
Angle α, β, γ (deg.)92.410, 103.030, 108.940
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Alcohol dehydrogenase E chain


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


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


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


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


Mass: 18.015 Da / Num. of mol.: 777 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 50 mM Tris-HCl buffer at pH 8.2, 18% (v/v) PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.43→37.94 Å / Num. obs: 119395 / % possible obs: 87.2 % / Redundancy: 7.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.023 / Rrim(I) all: 0.064 / Net I/σ(I): 19.7 / Num. measured all: 932809 / Scaling rejects: 3411
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
1.43-1.457.51.6714320657890.7540.6511.7951.485.5
7.83-37.947.90.025647282010.010.02793.398.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DWV

4dwv


Resolution: 1.43→37.94 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2082 5867 5 %
Rwork0.1895 111533 -
obs0.1905 117400 85.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.14 Å2 / Biso mean: 28.5543 Å2 / Biso min: 15.74 Å2
Refinement stepCycle: final / Resolution: 1.43→37.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 110 777 6457
Biso mean--22.78 37.63 -
Num. residues----748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0215868
X-RAY DIFFRACTIONf_angle_d2.6677949
X-RAY DIFFRACTIONf_dihedral_angle_d11.69856
X-RAY DIFFRACTIONf_chiral_restr0.254931
X-RAY DIFFRACTIONf_plane_restr0.014996
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 (%)
1.43-1.450.43261680.4323182335074
1.45-1.460.42131980.41083757395585
1.46-1.480.49571890.43683610379984
1.48-1.50.37591900.35593598378883
1.5-1.520.35021930.33263647384084
1.52-1.540.3811860.3443557374382
1.54-1.560.32971820.27413449363181
1.56-1.590.25931740.25253281345575
1.59-1.610.25911940.25133675386986
1.61-1.640.29762050.23533946415190
1.64-1.670.27762010.23323779398089
1.67-1.70.24562050.22623915412089
1.7-1.730.2412000.22173790399088
1.73-1.760.25092070.20183928413589
1.76-1.80.22771980.18323759395788
1.8-1.840.22092010.18853821402288
1.84-1.890.23331980.21233745394386
1.89-1.940.34711650.35643207337274
1.94-20.21671760.2073324350077
2-2.060.2142080.18853979418792
2.06-2.140.23422080.18523963417192
2.14-2.220.18022060.19153915412190
2.22-2.320.25041950.25163734392986
2.32-2.450.18472020.1633860406290
2.45-2.60.18622020.16563822402489
2.6-2.80.19651830.17353489367280
2.8-3.080.21082050.17143898410390
3.08-3.530.16292140.16694045425994
3.53-4.440.16882090.14433985419491
4.44-37.940.13642050.12633873407889
Refinement TLS params.Method: refined / Origin x: 17.6779 Å / Origin y: -12.4618 Å / Origin z: -20.683 Å
111213212223313233
T0.1822 Å20.0223 Å20.0021 Å2-0.1775 Å2-0.0026 Å2--0.2318 Å2
L0.3218 °20.1044 °2-0.1645 °2-0.2792 °2-0.1616 °2--1.2386 °2
S0.0181 Å °-0.0044 Å °-0.001 Å °-0.0696 Å °-0.0088 Å °-0.0324 Å °0.009 Å °-0.0272 Å °-0.0113 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 501
2X-RAY DIFFRACTION1allB1 - 501
3X-RAY DIFFRACTION1allS1 - 807

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