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- PDB-1ju9: HORSE LIVER ALCOHOL DEHYDROGENASE VAL292SER MUTANT -

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Basic information

Entry
Database: PDB / ID: 1ju9
TitleHORSE LIVER ALCOHOL DEHYDROGENASE VAL292SER MUTANT
ComponentsALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / ALCOHOL / NICOTINAMIDE COENZYME / MUTANT
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. / 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 / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRubach, J.K. / Ramaswamy, S. / Plapp, B.V.
Citation
Journal: Biochemistry / Year: 2001
Title: Contributions of valine-292 in the nicotinamide binding site of liver alcohol dehydrogenase and dynamics to catalysis.
Authors: Rubach, J.K. / Ramaswamy, S. / Plapp, B.V.
#1: Journal: Biochemistry / Year: 1999
Title: SUBSTITUTIONS IN THE FLEXIBLE LOOP OF HORSE LIVER ALCOHOL DEHYDROGENASE HINDER THE CONFORMATIONAL CHANGE AND UNMASK HYDROGEN TRANSFER
Authors: Ramaswamy, S. / Park, D.H. / Plapp, B.V.
#2: 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.
#3: Journal: J.Mol.Biol. / Year: 1981
Title: Structure of a Triclinic Ternary Complex of Horse Liver Alcohol Dehydrogenase at 2.9 Angstroms Resolution
Authors: Eklund, H. / Samama, J.-P. / Wallen, L. / Branden, C.-I. / Akeson, A. / A Jones, T.
#4: Journal: J.Mol.Biol. / Year: 1976
Title: Three-Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 Angstroms Resolution
Authors: Eklund, H. / Nordstrom, B. / Zeppezauer, E. / Soderlund, G. / Ohlsson, I. / Boiwe, T. / Soderberg, B.-O. / Tapia, O. / Branden, C.-I. / Akeson, A.
History
DepositionAug 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 11THE RECOMBINANT ENZYME WAS CRYSTALLIZED IN HANGING DROPS CONTAINING 50 MM AMMMONIUM ...THE RECOMBINANT ENZYME WAS CRYSTALLIZED IN HANGING DROPS CONTAINING 50 MM AMMMONIUM N[TRIS(HYDROXYMETHYL)METHYL]- AMINOMETHANESULFONATE BUFFER, PH 7.0, AT 5 DEG C, WITH 10.6 MM NAD+ AND 20 MM 2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL AND 9% MPD OVER A RESERVOIR WITH 18 % MPD. HOWEVER, ONLY THE ADP PORTION OF NAD+ WAS VISIBLE IN THE ELECTRON DENSITY MAPS. THE COORDINATES ONLY INCLUDE THE ADP.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALCOHOL DEHYDROGENASE
B: ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2718
Polymers79,6822
Non-polymers1,5886
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-104 kcal/mol
Surface area27660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.271, 180.398, 46.176
Angle α, β, γ (deg.)90.00, 106.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ALCOHOL DEHYDROGENASE / / ADH / ALCOHOL DEHYDROGENASE E CHAIN


Mass: 39841.223 Da / Num. of mol.: 2 / Mutation: V292S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Cellular location: CYTOPLASM / Gene: M64864 / Organ: LIVER / 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 / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 5 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlenzyme1drop
250 mMammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfonate buffer1droppH7.0
39 %MES1drop
410.6 mMNAD+1drop
520 mM2,3,4,5,6-pentafluorobenzyl alohol1drop
618 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 18, 2000 / Details: CONFOCAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→28.63 Å / Num. all: 41422 / Num. obs: 41422 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 11.4
Reflection shellResolution: 2.01→2.07 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.065 / Mean I/σ(I) obs: 8.9 / Rsym value: 0.065 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 41073 / % possible obs: 90.8 % / Num. measured all: 82843
Reflection shell
*PLUS
% possible obs: 84.9 %

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5refinement
CrystalClear(MSC/RIGAKU)data reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HLD

1hld


Resolution: 2→20 Å / SU B: 5.07 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.25 / ESU R Free: 0.19 / Stereochemistry target values: refmac 5.0 mon_lib
RfactorNum. reflection% reflectionSelection details
Rfree0.23158 1252 3.1 %RANDOM
Rwork0.19563 ---
all0.1956 41422 --
obs0.19673 41073 90.8 %-
Displacement parametersBiso mean: 28.007 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20 Å2-0.04 Å2
2---2.4 Å20 Å2
3---1.06 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5566 0 58 164 5788
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONp_bond_d0.0120.0225728
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.5261.9817754
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.7351.53702
X-RAY DIFFRACTIONp_mcangle_it1.3325986
X-RAY DIFFRACTIONp_scbond_it2.29532026
X-RAY DIFFRACTIONp_scangle_it3.7994.51768
X-RAY DIFFRACTIONp_plane_restr0.0050.024156
X-RAY DIFFRACTIONp_chiral_restr0.1020.2902
X-RAY DIFFRACTIONp_singtor_nbd4.0443746
X-RAY DIFFRACTIONp_multtor_nbd16.399151042
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1380.5553
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.278 72
Rwork0.228 2225
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 1.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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