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- PDB-5vl0: horse liver alcohol dehydrogenase complexed with NADH and N-benzy... -

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Basic information

Entry
Database: PDB / ID: 5vl0
Titlehorse liver alcohol dehydrogenase complexed with NADH and N-benzyformamide
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / N-benzylformamide / horse liver / NADH
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
N-BENZYLFORMAMIDE / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsPlapp, B.V. / Brown, E.N. / Ramaswamy, S. / Baskar Raj, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)AA00279 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM08365 United States
Citation
Journal: Biochemistry / Year: 2017
Title: Horse Liver Alcohol Dehydrogenase: Zinc Coordination and Catalysis.
Authors: Plapp, B.V. / Savarimuthu, B.R. / Ferraro, D.J. / Rubach, J.K. / Brown, E.N. / Ramaswamy, S.
#1: 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.
History
DepositionApr 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _citation_author.name
Revision 1.2Aug 2, 2017Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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.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
C: Alcohol dehydrogenase E chain
D: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,37522
Polymers159,4134
Non-polymers3,96218
Water24,2661347
1
A: Alcohol dehydrogenase E chain
B: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,68811
Polymers79,7072
Non-polymers1,9819
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-123 kcal/mol
Surface area26580 Å2
MethodPISA
2
C: Alcohol dehydrogenase E chain
D: Alcohol dehydrogenase E chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,68811
Polymers79,7072
Non-polymers1,9819
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-122 kcal/mol
Surface area26670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.160, 180.290, 86.920
Angle α, β, γ (deg.)90.000, 106.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Alcohol dehydrogenase E chain


Mass: 39853.273 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P00327, alcohol dehydrogenase

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Non-polymers , 5 types, 1365 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical
ChemComp-BNF / N-BENZYLFORMAMIDE


Mass: 135.163 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H9NO
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1347 / 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: 2.37 Å3/Da / Density % sol: 48.05 % / Description: long blocks
Crystal growTemperature: 278 K / Method: microdialysis / pH: 7
Details: 10 mg/ml enzyme dialyzed against 50 mM ammonium N-[tris(hydroxylmethyl)methyl]2-aminoethane sulfonate (pH 6.7 at 25 deg C) with 1 mM NADH and 10 mM N-benzylformamide as the concentration of ...Details: 10 mg/ml enzyme dialyzed against 50 mM ammonium N-[tris(hydroxylmethyl)methyl]2-aminoethane sulfonate (pH 6.7 at 25 deg C) with 1 mM NADH and 10 mM N-benzylformamide as the concentration of 2-methyl-2,4-pentanediol was raised to 25 %. Crystas was mounted on a fiber loop and flash vitrified by plunging it into liquid N2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→19.95 Å / Num. obs: 365139 / % possible obs: 79.4 % / Redundancy: 6.19 % / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.094 / Χ2: 1.14 / Net I/σ(I): 8.3 / Num. measured all: 2278017 / Scaling rejects: 17086
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) allΧ2% possible all
1.2-1.244.340.5131.7239880.5761.3359.5
1.24-1.295.160.442.10.4861.376.4
1.29-1.355.510.3792.60.4151.3278.9
1.35-1.425.350.3123.20.3421.377.5
1.42-1.515.160.2523.80.2781.2675.7
1.51-1.635.390.2464.30.2691.375.6
1.63-1.796.10.2135.40.231.1977.3
1.79-2.057.660.1658.40.1751.0683.6
2.05-2.587.190.10212.30.1090.990.7
2.58-19.958.60.06620.80.070.9398.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
d*TREK9.9.9.8Ldata scaling
MOLREPphasing
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
Omodel building
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P1R

1p1r


Resolution: 1.2→19.95 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.849 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.049
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1985 3775 1 %RANDOM
Rwork0.1582 ---
obs0.1586 361271 79.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 77.67 Å2 / Biso mean: 20.318 Å2 / Biso min: 10.13 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20 Å20.19 Å2
2---1.76 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.2→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11140 0 240 1357 12737
Biso mean--19.35 32.6 -
Num. residues----1496
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0211812
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211437
X-RAY DIFFRACTIONr_angle_refined_deg2.0612.01316008
X-RAY DIFFRACTIONr_angle_other_deg1.089326657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26651519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88224.392403
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.714152096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7771551
X-RAY DIFFRACTIONr_chiral_restr0.1280.21877
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02112783
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022204
X-RAY DIFFRACTIONr_rigid_bond_restr3.996323249
X-RAY DIFFRACTIONr_sphericity_free19.855863
X-RAY DIFFRACTIONr_sphericity_bonded6.595523514
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 180 -
Rwork0.282 19254 -
all-19434 -
obs--57.35 %

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