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- PDB-1ykf: NADP-DEPENDENT ALCOHOL DEHYDROGENASE FROM THERMOANAEROBIUM BROCKII -

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Basic information

Entry
Database: PDB / ID: 1ykf
TitleNADP-DEPENDENT ALCOHOL DEHYDROGENASE FROM THERMOANAEROBIUM BROCKII
ComponentsNADP-DEPENDENT ALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


isopropanol dehydrogenase (NADP+) / isopropanol dehydrogenase (NADP+) activity / zinc ion binding
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADP-dependent isopropanol dehydrogenase
Similarity search - Component
Biological speciesThermoanaerobacter brockii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsKorkhin, Y. / Frolow, F.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: NADP-dependent bacterial alcohol dehydrogenases: crystal structure, cofactor-binding and cofactor specificity of the ADHs of Clostridium beijerinckii and Thermoanaerobacter brockii.
Authors: Korkhin, Y. / Kalb(Gilboa), A.J. / Peretz, M. / Bogin, O. / Burstein, Y. / Frolow, F.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystalline Alcohol Dehydrogenases from the Mesophilic Bacterium Clostridium Beijerinckii and the Thermophilic Bacterium Thermoanaerobium Brockii: Preparation, Characterization and Molecular Symmetry
Authors: Korkhin, Y. / Frolow, F. / Bogin, O. / Peretz, M. / Kalb(Gilboa), A.J. / Burstein, Y.
History
DepositionMar 25, 1996Processing site: BNL
Revision 1.0Jan 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / 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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADP-DEPENDENT ALCOHOL DEHYDROGENASE
B: NADP-DEPENDENT ALCOHOL DEHYDROGENASE
C: NADP-DEPENDENT ALCOHOL DEHYDROGENASE
D: NADP-DEPENDENT ALCOHOL DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,01512
Polymers150,7794
Non-polymers3,2358
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20770 Å2
ΔGint-256 kcal/mol
Surface area44700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.614, 80.614, 400.335
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.51537, -0.855639, -0.047698), (-0.855787, -0.516783, 0.023751), (-0.044972, 0.028578, -0.998579)34.28347, 60.76212, 1.64316
2given(-0.863898, 0.213444, 0.456205), (0.214704, -0.663285, 0.716907), (0.455613, 0.717283, 0.527183)71.396, 19.91022, -30.98194
3given(-0.638898, 0.644718, -0.419701), (0.656234, 0.172043, -0.734683), (-0.401456, -0.744809, -0.533004)55.14186, -11.97971, 29.1296

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Components

#1: Protein
NADP-DEPENDENT ALCOHOL DEHYDROGENASE


Mass: 37694.871 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: HOLO-ENZYME FORM / Source: (gene. exp.) Thermoanaerobacter brockii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P14941, alcohol dehydrogenase (NADP+)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 32 %
Crystal growpH: 8.2 / Details: pH 8.2
Crystal grow
*PLUS
Temperature: 293 K / pH: 8.3 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16.8 mg/mlprotein1drop
22 mMNADP+1drop
350 mMTris-HCl1drop
450 mM1dropNaCl
50.1 mMdithiothreitol1drop
60.05 mM1dropZnCl2
714 %PEG40001drop
815.5 %PEG40001reservoir
950 mM1reservoirNaCl
1050 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Apr 27, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→33 Å / Num. obs: 44669 / % possible obs: 88.4 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 16.3
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 1.93 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 4.3 / % possible all: 75.8
Reflection shell
*PLUS
% possible obs: 75.8 % / Num. unique obs: 2547

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
HKL(DENZO)data reduction
HKL(SCALEPACK)data scaling
X-PLOR3.1phasing
RefinementResolution: 2.5→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.267 -3.4 %
Rwork0.215 --
obs0.215 43359 -
Displacement parametersBiso mean: 36.75 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10569 0 196 43 10808
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.484
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.309
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 44669
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.309

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