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- PDB-6owp: Horse liver F93W alcohol dehydrogenase complexed with NAD and tri... -

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Basic information

Entry
Database: PDB / ID: 6owp
TitleHorse liver F93W alcohol dehydrogenase complexed with NAD and trifluoroethanol
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / NAD / 2 / 2-trifluoretanol / Phe93 to Trp substitution / Horse liver E enzyme
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. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / 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 / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIFLUOROETHANOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsPlapp, B.V.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)AA00279 United States
Department of Health & Human Services (HHS)GM078446 United States
Citation
Journal: Biochemistry / Year: 2020
Title: Substitutions of Amino Acid Residues in the Substrate Binding Site of Horse Liver Alcohol Dehydrogenase Have Small Effects on the Structures but Significantly Affect Catalysis of Hydrogen Transfer.
Authors: Kim, K. / Plapp, B.V.
#1: Journal: Biochemistry / Year: 1993
Title: Unmasking of hydrogen tunneling in the horse liver alcohol dehydrogenase reaction by site-directed mutagenesis.
Authors: Bahnson, B.J. / Park, D.H. / Kim, K. / Plapp, B.V. / Klinman, J.P.
#2: Journal: Biochemistry / Year: 2012
Title: Atomic-resolution structures of horse liver alcohol dehydrogenase with NAD(+) and fluoroalcohols define strained Michaelis complexes.
Authors: Plapp, B.V. / Ramaswamy, S.
#3: Journal: Isotope Effects in Chemistry and Biology / Year: 2006
Title: Catalysis by Alcohol Dehydrogenases
Authors: Plapp, B.V.
#4: Journal: Chem. Biol. Interact. / Year: 2017
Title: Inversion of substrate stereoselectivity of horse liver alcohol dehydrogenase by substitutions of Ser-48 and Phe-93.
Authors: Kim, K. / Plapp, B.V.
#5: Journal: Biochemistry / Year: 1998
Title: Active site modifications in a double mutant of liver alcohol dehydrogenase: structural studies of two enzyme-ligand complexes.
Authors: Colby, T.D. / Bahnson, B.J. / Chin, J.K. / Klinman, J.P. / Goldstein, B.M.
#6: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 1997
Title: A link between protein structure and enzyme catalyzed hydrogen tunneling.
Authors: Bahnson, B.J. / Colby, T.D. / Chin, J.K. / Goldstein, B.M. / Klinman, J.P.
History
DepositionMay 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)81,92813
Polymers79,7852
Non-polymers2,14311
Water18,4471024
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-115 kcal/mol
Surface area26540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.280, 51.200, 92.310
Angle α, β, γ (deg.)92.120, 102.980, 110.040
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: 39892.309 Da / Num. of mol.: 2 / Mutation: F93W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Organ: liver / Production host: Escherichia coli (E. coli) / Variant (production host): XL1-Blue / References: UniProt: P00327, alcohol dehydrogenase

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Non-polymers , 5 types, 1035 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAJ / NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM)


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ETF / TRIFLUOROETHANOL


Mass: 100.040 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3F3O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1024 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 298 K / Method: microdialysis / pH: 7
Details: 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanne sulfonate, pH 6.7 (at 25 deg C), 0,25 mM EDTA, 10 mg/ml protein, 1 mM NAD+, 100 mM 2,2,2-trifluoroethanol, 12-15 % 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.827 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 3, 2008 / Details: Rosenbaum-Rock vertically focussed mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.827 Å / Relative weight: 1
ReflectionResolution: 1.14→19.97 Å / Num. obs: 244957 / % possible obs: 91.2 % / Redundancy: 3.71 % / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.057 / Χ2: 1.18 / Net I/σ(I): 12.2 / Num. measured all: 914787 / Scaling rejects: 6861
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRrim(I) allΧ2Rejects% possible all
1.14-1.183.440.2563.454912157980.3021.1953358.8
1.18-1.233.420.2463.478415226830.2911.1889684.4
1.23-1.283.840.2184.397690253430.2541.1740094.4
1.28-1.353.860.1815.598702255130.211.210694.9
1.35-1.443.850.1417.198729255820.1631.1813895.4
1.44-1.553.820.1079.398716257620.1241.1728595.9
1.55-1.73.770.08212.298089259270.0961.126696.2
1.7-1.953.710.06415.396888259660.0751.0647196.9
1.95-2.453.570.05120.594391261030.061.15128897.1
2.45-19.973.640.0333698255262800.0391.38247897.9

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Processing

Software
NameVersionClassification
d*TREK9.9.9.8Ldata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
d*TREKdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6owm

6owm


Resolution: 1.14→19.97 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.896 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.029
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1421 2481 1 %RANDOM
Rwork0.1219 ---
obs0.1221 242456 91.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 61.1 Å2 / Biso mean: 13.986 Å2 / Biso min: 6.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å2-0.31 Å20.27 Å2
2--0.16 Å20.08 Å2
3----0.54 Å2
Refinement stepCycle: final / Resolution: 1.14→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5576 0 148 1055 6779
Biso mean--14.98 27.7 -
Num. residues----748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0136250
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176049
X-RAY DIFFRACTIONr_angle_refined_deg1.8931.6868518
X-RAY DIFFRACTIONr_angle_other_deg1.5611.59214170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg17.3985.366834
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88723.178236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.047151121
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5671525
X-RAY DIFFRACTIONr_chiral_restr0.1110.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027574
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021147
X-RAY DIFFRACTIONr_rigid_bond_restr2.322312297
LS refinement shellResolution: 1.14→1.17 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 129 -
Rwork0.231 11093 -
all-11222 -
obs--56.39 %

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