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- PDB-1a72: AN ACTIVE-SITE DOUBLE MUTANT (PHE93->TRP, VAL203->ALA) OF HORSE L... -

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Basic information

Entry
Database: PDB / ID: 1a72
TitleAN ACTIVE-SITE DOUBLE MUTANT (PHE93->TRP, VAL203->ALA) OF HORSE LIVER ALCOHOL DEHYDROGENASE IN COMPLEX WITH THE ISOSTERIC NAD ANALOG CPAD
ComponentsHORSE LIVER ALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE (NAD(A)-CHOH(D)) / ACTIVE SITE MUTANT / LIVER ALCOHOL DEHYDROGENASE / ISOSTERIC NAD INHIBITORS
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
Chem-PAD / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsColby, T.D. / Bahnson, B.J. / Chin, J.K. / Klinman, J.P. / Goldstein, B.M.
Citation
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.
#1: Journal: Proc.Natl.Acad.Sci.USA / 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
DepositionMar 19, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _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 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HORSE LIVER ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6594
Polymers39,8641
Non-polymers7943
Water1,40578
1
A: HORSE LIVER ALCOHOL DEHYDROGENASE
hetero molecules

A: HORSE LIVER ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,3178
Polymers79,7292
Non-polymers1,5886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5650 Å2
ΔGint-112 kcal/mol
Surface area26460 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.500, 74.200, 179.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein HORSE LIVER ALCOHOL DEHYDROGENASE


Mass: 39864.258 Da / Num. of mol.: 1 / Mutation: F93W, V203A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: F93W V203ALADH / Organ: LIVER / Plasmid: PHAGEMID PBPP-LADH / Cellular location (production host): CYTOPLASM / Gene (production host): F93W,V203ALADH / 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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PAD / 5-BETA-D-RIBOFURANOSYLPICOLINAMIDE ADENINE-DINUCLEOTIDE / CPAD


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: CRYSTALS GROWN FROM 4 MICROLITER HANGING DROPS OF 10MG/ML PROTEIN IN 50 MM TRIS BUFFER (PH8.4 @4C) 4% (V/V) ETOH EQUILIBRATED AT 4C WITH WELLS CONTAINING 11-13% ETOH, vapor diffusion - ...Details: CRYSTALS GROWN FROM 4 MICROLITER HANGING DROPS OF 10MG/ML PROTEIN IN 50 MM TRIS BUFFER (PH8.4 @4C) 4% (V/V) ETOH EQUILIBRATED AT 4C WITH WELLS CONTAINING 11-13% ETOH, vapor diffusion - hanging drop, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113 mg/mlprotein1drop
250 mMTris-HCl1drop
34 %(v/v)PEG4001drop
45 mMNAD1drop
550 mMTris-HCl1reservoir
618 %(v/v)PEG4001reservoir

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Data collection

DiffractionMean temperature: 275 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Dec 15, 1993
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→22 Å / Num. obs: 10388 / % possible obs: 76.9 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 6
Reflection shellResolution: 2.56→2.68 Å / Mean I/σ(I) obs: 2 / % possible all: 43
Reflection
*PLUS
Num. measured all: 16939 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 43 %

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
XDSdata reduction
X-GENdata scaling
X-PLOR3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 8ADH

8adh


Resolution: 2.6→8 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: A POSTERIORI / σ(F): 2
Details: RFREE FIGURE BELONGS TO SA OMIT PROCEDURE USED TO CONFIRM FIT OF LIGAND. THIS RFREE DESCRIBES A MODEL NOT CONTAINING SOLVENT
RfactorNum. reflection% reflectionSelection details
Rfree0.3 1072 10 %RANDOM
Rwork0.176 ---
obs0.176 10388 76.9 %-
Displacement parametersBiso mean: 16.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2786 0 46 78 2910
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.6
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.431.5
X-RAY DIFFRACTIONx_mcangle_it2.232
X-RAY DIFFRACTIONx_scbond_it2.242
X-RAY DIFFRACTIONx_scangle_it3.292.5
LS refinement shellResolution: 2.6→2.71 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.309 55 10 %
Rwork0.234 543 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.6
LS refinement shell
*PLUS
Rfactor obs: 0.234

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