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- PDB-1a71: TERNARY COMPLEX OF AN ACTIVE SITE DOUBLE MUTANT OF HORSE LIVER AL... -

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Basic information

Entry
Database: PDB / ID: 1a71
TitleTERNARY COMPLEX OF AN ACTIVE SITE DOUBLE MUTANT OF HORSE LIVER ALCOHOL DEHYDROGENASE, PHE93=>TRP, VAL203=>ALA WITH NAD AND TRIFLUOROETHANOL
ComponentsLIVER ALCOHOL DEHYDROGENASEAlcohol dehydrogenase
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE (NAD(A)-CHOH(D)) / LIVER / ALCOHOL / DEHYDROGENASE / LADH / ACTIVE SITE MUTANT
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / all-trans-retinol dehydrogenase (NAD+) activity / alcohol dehydrogenase / retinol metabolic process / retinoic acid 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
TRIFLUOROETHANOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alcohol dehydrogenase E chain
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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_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 / _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: LIVER ALCOHOL DEHYDROGENASE
B: LIVER ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,51710
Polymers79,7292
Non-polymers1,7898
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-113 kcal/mol
Surface area26090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.600, 44.100, 92.600
Angle α, β, γ (deg.)103.00, 87.90, 70.70
Int Tables number1
Space group name H-MP1

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Components

#1: Protein LIVER ALCOHOL DEHYDROGENASE / Alcohol dehydrogenase


Mass: 39864.258 Da / Num. of mol.: 2 / Mutation: F93W, V203A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Cellular location: CYTOPLASM / Gene: LADH F93W V203A / Organ: LIVER / Plasmid: PHAGEMID PBPP-LADH / Cellular location (production host): CYTOPLASM / Gene (production host): LADH F93W,V203A / 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: Chemical ChemComp-ETF / TRIFLUOROETHANOL / 2,2,2-Trifluoroethanol


Mass: 100.040 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3F3O
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.3 Å3/Da / Density % sol: 47.99 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.4
Details: 4MICROLITER HANGING DROPS TRIS PH 8.4 AT 4C, 5MM TRIFLUROETHANOL, 4% PEG400 EQUILIBRATED AGAINST WELLS CONTAINING 5MM TFE AND 18%PEG 400, vapor diffusion - hanging drop
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: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 1, 1996 / Details: YALE MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 38046 / % possible obs: 77.1 % / Observed criterion σ(I): 2 / Redundancy: 1.7 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 7.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2 / % possible all: 42.3
Reflection
*PLUS
Num. measured all: 77199
Reflection shell
*PLUS
% possible obs: 42.3 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OHX

2ohx


Resolution: 2→10 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED
Cross valid method: UP TO LAST CG MINIMIZATION THROUGHOUT UNTIL LAST CG REFINEMENT
σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.288 3781 10 %RANDOM
Rwork0.199 ---
obs0.199 37755 77.1 %-
Displacement parametersBiso mean: 22.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å2-0.95 Å2-0.92 Å2
2---0.02 Å21.48 Å2
3----0.46 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5572 0 104 179 5855
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.38
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.991.5
X-RAY DIFFRACTIONx_mcangle_it2.742
X-RAY DIFFRACTIONx_scbond_it3.552
X-RAY DIFFRACTIONx_scangle_it5.072.5
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.353 322 10 %
Rwork0.268 2825 -
obs--51 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / 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_deg24
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4
LS refinement shell
*PLUS
Rfactor obs: 0.268

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