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- PDB-6owm: Horse liver F93W alcohol dehydrogenase complexed with NAD and pen... -

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Basic information

Entry
Database: PDB / ID: 6owm
TitleHorse liver F93W alcohol dehydrogenase complexed with NAD and pentafluorobenzyl alcohol
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / NAD / pentafluorobenzyl alcohol / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) / 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 1.1Dec 11, 2019Group: Database references / Category: pdbx_database_related / pdbx_related_exp_data_set / Item: _pdbx_database_related.details
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 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 1.4Mar 11, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Oct 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.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)82,12413
Polymers79,7852
Non-polymers2,33911
Water18,4471024
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-112 kcal/mol
Surface area26760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.470, 51.440, 92.560
Angle α, β, γ (deg.)92.09, 102.95, 110.25
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) / 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-PFB / 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL


Mass: 198.090 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H3F5O / 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 / Feature type: SUBJECT OF INVESTIGATION / 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: 2.41 Å3/Da / Density % sol: 48.91 % / Description: block
Crystal growTemperature: 298 K / Method: microdialysis / pH: 7
Details: 10 mg/ml protein, 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethane sulfonate, 0.25 mM EDTA, pH 6.7 at 25 deg C, 1 mM NAD+, 10 mM 2,3,4,5,6-pentafluorobenzyl alcohol, 14 to 25 % 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2007 / Details: adjustable foculs K-B pari SiPlus PT, RH coatings
RadiationMonochromator: double crystal cryocooled Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.1→19.62 Å / Num. obs: 267734 / % possible obs: 88.6 % / Redundancy: 5.15 % / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.082 / Χ2: 1.15 / Net I/σ(I): 11.4 / Num. measured all: 1394329 / Scaling rejects: 16553
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRrim(I) allΧ2Rejects% possible all
1.1-1.143.440.283.159197171940.3291.444456.8
1.14-1.183.530.2023.993072263430.2371.242787.4
1.18-1.243.830.1674.8103993271690.1941.191889.8
1.24-1.33.840.1445.6105191273970.1671.145990.7
1.3-1.393.850.1216.7107187277970.141.0917191.7
1.39-1.493.870.1057.4108886280340.1220.9328392.8
1.49-1.646.730.1548.9191695283530.1671.2389993.9
1.64-1.887.740.09713.8225658287830.1041.11292195.4
1.88-2.377.570.07219.4227174292150.0771.12605396.6
2.37-19.626.050.06221172276274490.0691.2607890.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
d*TREK9.9.9.8Ldata scaling
PDB_EXTRACT3.25data extraction
REFMACphasing
Omodel building
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6o91

6o91


Resolution: 1.1→19.62 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.979 / SU B: 0.742 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.027 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.14059 2622 1 %RANDOM
Rwork0.12386 ---
obs0.12402 265082 88.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.811 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0.54 Å20.31 Å2
2--0.46 Å20.12 Å2
3----0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.1→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5576 0 142 1024 6742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0136273
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176067
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.6888549
X-RAY DIFFRACTIONr_angle_other_deg1.5411.59114211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg17.8445.377836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79423.178236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.888151124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5311525
X-RAY DIFFRACTIONr_chiral_restr0.1070.2865
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027608
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021149
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9871.3743143
X-RAY DIFFRACTIONr_mcbond_other0.9851.3733142
X-RAY DIFFRACTIONr_mcangle_it1.2042.0713944
X-RAY DIFFRACTIONr_mcangle_other1.2042.0713945
X-RAY DIFFRACTIONr_scbond_it1.6761.6463130
X-RAY DIFFRACTIONr_scbond_other1.6751.6473131
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9452.3714585
X-RAY DIFFRACTIONr_long_range_B_refined2.58918.7417225
X-RAY DIFFRACTIONr_long_range_B_other2.16517.3786884
X-RAY DIFFRACTIONr_rigid_bond_restr2.481312338
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.1→1.128 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 123 -
Rwork0.285 11720 -
obs--53.11 %

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