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- PDB-1axe: CRYSTAL STRUCTURE OF THE ACTIVE-SITE MUTANT PHE93->TRP OF HORSE L... -

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Entry
Database: PDB / ID: 1axe
TitleCRYSTAL STRUCTURE OF THE ACTIVE-SITE MUTANT PHE93->TRP OF HORSE LIVER ALCOHOL DEHYDROGENASE IN COMPLEX WITH NAD AND INHIBITOR TRIFLUOROETHANOL
ComponentsALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE (NAD(A)-CHOH(D)) / ALCOHOL DEHYDROGENASE
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
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. / Chin, J.K. / Goldstein, B.M.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Refined Crystal Structure of Liver Alcohol Dehydrogenase-Nadh Complex at 1.8 A Resolution
Authors: Al-Karadaghi, S. / Cedergren-Zeppezauer, E.S. / Hovmoller, S. / Petratos, K. / Terry, H. / Wilson, K.S.
#2: Journal: J.Biol.Chem. / Year: 1986
Title: Interdomain Motion in Liver Alcohol Dehydrogenase. Structural and Energetic Analysis of the Hinge Bending Mode
Authors: Colonna-Cesari, F. / Perahia, D. / Karplus, M. / Eklund, H. / Branden, C.I. / Tapia, O.
#3: Journal: Biochemistry / Year: 1984
Title: Crystallographic Investigations of Nicotinamide Adenine Dinucleotide Binding to Horse Liver Alcohol Dehydrogenase
Authors: Eklund, H. / Samama, J.P. / Jones, T.A.
#4: Journal: Biochemistry / Year: 1983
Title: Crystal-Structure Determination of Reduced Nicotinamide Adenine Dinucleotide Complex with Horse Liver Alcohol Dehydrogenase Maintained in its Apo Conformation by Zinc-Bound Imidazole
Authors: Cedergren-Zeppezauer, E.
#5: Journal: J.Biol.Chem. / Year: 1983
Title: Three-Dimensional Structure of Isonicotinimidylated Liver Alcohol Dehydrogenase
Authors: Plapp, B.V. / Eklund, H. / Jones, T.A. / Branden, C.I.
#6: Journal: Proc.Natl.Acad.Sci.USA / Year: 1983
Title: Crystal Structures of the Active Site in Specifically Metal-Depleted and Cobalt-Substituted Horse Liver Alcohol Dehydrogenase Derivatives
Authors: Schneider, G. / Eklund, H. / Cedergren-Zeppezauer, E. / Zeppezauer, M.
#7: Journal: Biochemistry / Year: 1982
Title: Pyrazole Binding in Crystalline Binary and Ternary Complexes with Liver Alcohol Dehydrogenase
Authors: Eklund, H. / Samama, J.P. / Wallen, L.
#8: Journal: Biochemistry / Year: 1982
Title: Crystal Structure Determinations of Coenzyme Analogue and Substrate Complexes of Liver Alcohol Dehydrogenase. Binding of 1,4,5,6-Tetrahydronicotinamide Adenine Dinucleotide and Trans-4-(N,N- ...Title: Crystal Structure Determinations of Coenzyme Analogue and Substrate Complexes of Liver Alcohol Dehydrogenase. Binding of 1,4,5,6-Tetrahydronicotinamide Adenine Dinucleotide and Trans-4-(N,N-Dimethylamino)Cinnamaldehyde to the Enzyme
Authors: Cedergren-Zeppezauer, E. / Samama, J.P. / Eklund, H.
#9: 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.
#10: Journal: J.Biol.Chem. / Year: 1979
Title: Structural Differences between Apo-and Holoenzyme of Horse Liver Alcohol Dehydrogenase
Authors: Eklund, H. / Branden, C.I.
#11: 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.
History
DepositionOct 15, 1997Processing site: BNL
Revision 1.0Apr 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)81,57310
Polymers79,7852
Non-polymers1,7898
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-111 kcal/mol
Surface area26600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.820, 44.580, 93.280
Angle α, β, γ (deg.)103.10, 87.59, 70.55
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.122993, 0.984919, 0.121686), (0.984696, -0.136373, 0.108516), (0.123474, 0.106477, -0.986619)
Vector: -0.3405, 0.2647, 0.9438)

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Components

#1: Protein ALCOHOL DEHYDROGENASE


Mass: 39892.309 Da / Num. of mol.: 2 / Mutation: F93W
Source method: isolated from a genetically manipulated source
Details: HOLO-ENZYME / Source: (gene. exp.) Equus caballus (horse) / Cellular location: CYTOPLASM / Gene: LADH CDNA / Organ: LIVER / Plasmid: PBPP-LADH / Cellular location (production host): CYTOPLASM / Gene (production host): LADH CDNA / 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-ETF / TRIFLUOROETHANOL


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


Mass: 18.015 Da / Num. of mol.: 116 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 49.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: CRYSTALS WERE GROWN FROM HANGING DROPS. THE INITIAL DROP CONTAINING 16MG/ML PROTEIN, A 10X EXCESS OF NAD, 5MM TRIFLUOROETHANOL AND 5% V/V OF PEG400 IN 50MM TRIS-HCL PH 8.4 WERE EQUILIBRATED ...Details: CRYSTALS WERE GROWN FROM HANGING DROPS. THE INITIAL DROP CONTAINING 16MG/ML PROTEIN, A 10X EXCESS OF NAD, 5MM TRIFLUOROETHANOL AND 5% V/V OF PEG400 IN 50MM TRIS-HCL PH 8.4 WERE EQUILIBRATED AT 4 DEGREES C OVER WELLS OF SIMILAR COMPOSITION CONTAINING 15-17% PEG400., vapor diffusion - hanging drop, temperature 277K
Crystal
*PLUS
Density % sol: 51 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
116 mg/mlprotein1drop
210 MNAD+1drop
35 mMtrifluoroethanol1drop
45 %(v/v)PEG4001drop
550 mMTris-HCl1reservoirpH8.4
65 mMtrifluoroethanol1reservoir
715-17 %(v/v)PEG4001reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 17, 1995 / Details: MONOCHROMATOR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→99 Å / Num. obs: 43756 / % possible obs: 85.2 % / Observed criterion σ(I): 2 / Redundancy: 1.83 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 5
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.31 / % possible all: 64.6

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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: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.269 4128 10 %RANDOM
Rwork0.203 ---
obs0.203 41054 67.6 %-
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5576 0 104 116 5796
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.85
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.47
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19.PEP
X-RAY DIFFRACTION2PARAM.NADTOPOLOGY.NAD
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.47

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