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- PDB-1qv7: HORSE LIVER ALCOHOL DEHYDROGENASE HIS51GLN/LYS228ARG MUTANT COMPL... -

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Basic information

Entry
Database: PDB / ID: 1qv7
TitleHORSE LIVER ALCOHOL DEHYDROGENASE HIS51GLN/LYS228ARG MUTANT COMPLEXED WITH NAD+ AND 2,3-DIFLUOROBENZYL ALCOHOL
ComponentsAlcohol dehydrogenase E chain
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / ALCOHOL / NICOTINAMIDE COENZYME / 2 / 3-DIFLUOROBENZYL ALCOHOL / HIS51GLN/LYS228ARG MUTANT / HORSE LIVER
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
2,3-DIFLUOROBENZYL ALCOHOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLebrun, L.A. / Park, D.-H. / Ramaswamy, S. / Plapp, B.V.
Citation
Journal: Biochemistry / Year: 2004
Title: Participation of histidine-51 in catalysis by horse liver alcohol dehydrogenase.
Authors: LeBrun, L.A. / Park, D.-H. / Ramaswamy, S. / Plapp, B.V.
#1: Journal: Biochemistry / Year: 1994
Title: Structures of Liver Alcohol Dehydrogenase Complexed with Nad+ and Substituted Benzyl Alcohols.
Authors: Ramaswamy, S. / Eklund, H. / Plapp, B.V.
#2: Journal: Biochemistry / Year: 1999
Title: Control of Coenzyme Binding to Horse Liver Alcohol Dehydrogenase.
Authors: LeBrun, L.A. / Plapp, B.V.
#3: Journal: Biochemistry / Year: 2002
Title: Mobility of Fluorobenzyl Alcohols Bound to Liver Alcohol Dehydrogenase as Determined by NMR and X-Ray Crystallographic Studies.
Authors: Rubach, J.K. / Plapp, B.V.
#4: Journal: J.Mol.Biol. / Year: 1981
Title: Structure of a Triclinic Ternary Complex of Horse Liver Alcohol Dehydrogenase at 2.9 A Resolution
Authors: Eklund, H. / Samama, J.-P. / Wallen, L. / Branden, C.-I. / Akeson, A. / Jones, T.A.
#5: Journal: J.Mol.Biol. / Year: 1976
Title: Three-Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 A Resolution
Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.O. / Tapia, O. / Branden, C.-I. / Akeson, A.
#6: Journal: J.Biol.Chem. / Year: 1982
Title: Binding of Substrate in a Ternary Complex of Horse Liver Alcohol Dehydrogenase
Authors: Eklund, H. / Plapp, B.V. / Samama, J.-P. / Branden, C.-I.
History
DepositionAug 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
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_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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 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)81,61910
Polymers79,7432
Non-polymers1,8778
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-106 kcal/mol
Surface area26320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.050, 50.962, 92.466
Angle α, β, γ (deg.)91.61, 103.03, 109.86
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

#1: Protein Alcohol dehydrogenase E chain


Mass: 39871.270 Da / Num. of mol.: 2
Fragment: Recombinant enzyme without the N-acetyl group found in natural enzyme
Mutation: H51Q and K228R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Plasmid: pBPP / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / 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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-DFB / 2,3-DIFLUOROBENZYL ALCOHOL / 2 / 3-difluorobenzyl alcohol


Mass: 144.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6F2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 48.07 %
Crystal growTemperature: 278 K / Method: dialysis / pH: 7
Details: 50 mM ammonium N-[tris(hydroxymethyl)methyl)]-2-aminoethanesulfonate buffer, 1 mM NAD+, 10 mM 2,3-difluorobenzyl alcohol, 2-methyl-2,4-pentanediol, pH 7.0, dialysis, temperature 278K
Crystal grow
*PLUS
Temperature: 5 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlenzyme11
250 mMTES11pH7.0
31 mMNAD+11
410 mM2,3-difluorobenzyl alcohol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.03 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 25, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 67918 / Num. obs: 67918 / % possible obs: 95.1 % / Redundancy: 1.95 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 7.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.06 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.72 / Num. unique all: 8849 / % possible all: 91.9
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 132501
Reflection shell
*PLUS
% possible obs: 94.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
REFMAC5refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1hld

1hld


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.341 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22205 1608 2.5 %RANDOM
Rwork0.17732 ---
all0.1784 62982 --
obs0.17845 62982 95.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.007 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å2-0.96 Å20.66 Å2
2--0.73 Å20.49 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5572 0 112 489 6173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0225790
X-RAY DIFFRACTIONr_bond_other_d0.0020.025362
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.9937842
X-RAY DIFFRACTIONr_angle_other_deg1.49312544
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7473746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.667151059
X-RAY DIFFRACTIONr_chiral_restr0.110.2918
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026320
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021076
X-RAY DIFFRACTIONr_nbd_refined0.220.31196
X-RAY DIFFRACTIONr_nbd_other0.2090.35431
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.5565
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0840.54
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.310
X-RAY DIFFRACTIONr_symmetry_vdw_other0.250.325
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2960.514
X-RAY DIFFRACTIONr_mcbond_it1.0331.53704
X-RAY DIFFRACTIONr_mcangle_it1.80225990
X-RAY DIFFRACTIONr_scbond_it2.99732086
X-RAY DIFFRACTIONr_scangle_it4.9824.51852
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.293 107
Rwork0.232 4625
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.8

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