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- PDB-1kev: STRUCTURE OF NADP-DEPENDENT ALCOHOL DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 1kev
TitleSTRUCTURE OF NADP-DEPENDENT ALCOHOL DEHYDROGENASE
ComponentsNADP-DEPENDENT ALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / ZINC / NADP
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
Chem-NDP / NADP-dependent isopropanol dehydrogenase
Similarity search - Component
Biological speciesClostridium beijerinckii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKorkhin, Y. / Frolow, F.
CitationJournal: 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, A.J. / Burstein, Y.
History
DepositionOct 21, 1996Processing site: BNL
Revision 1.0Oct 22, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 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: 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)154,29512
Polymers151,0524
Non-polymers3,2438
Water12,358686
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20240 Å2
ΔGint-294 kcal/mol
Surface area46190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.450, 151.420, 127.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.453609, 0.17899, 0.873042), (0.17898, -0.941369, 0.285991), (0.873044, 0.285985, 0.394978)24.92539, 45.55451, -24.93938
2given(0.351881, -0.591666, -0.725335), (-0.591639, -0.741063, 0.317474), (-0.725357, 0.317423, -0.610819)65.25851, 68.24573, 65.95944
3given(-0.898293, 0.413657, -0.148181), (0.413621, 0.682257, -0.602863), (-0.148281, -0.602838, -0.783964)65.10555, 11.80437, 77.60818

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Components

#1: Protein
NADP-DEPENDENT ALCOHOL DEHYDROGENASE


Mass: 37762.891 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: HOLO-ENZYME FORM / Source: (gene. exp.) Clostridium beijerinckii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P25984, 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-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / 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: 2.94 Å3/Da / Density % sol: 32 %
Crystal growpH: 8.2 / Details: SEE REFERENCE 1, pH 8.2
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16.5 mg/mlenzyme1drop
21.5 mMNADP+1drop
310.5 %PEG40001drop
450 mM1dropNaCl
550 mMTris-HCl1drop
611.5 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.2748
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 22, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2748 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 97572 / % possible obs: 88.2 % / Observed criterion σ(I): 0 / Redundancy: 3.33 % / Biso Wilson estimate: 27.5 Å2 / Rsym value: 0.058 / Net I/σ(I): 18.1
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.97 % / Mean I/σ(I) obs: 3.19 / Rsym value: 0.232 / % possible all: 69.3

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Processing

Software
NameVersionClassification
REPLACEmodel building
X-PLOR3.1refinement
HKL(DENZO)data reduction
HKL(SCALEPACK)data scaling
REPLACEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PED

1ped


Resolution: 2.05→50 Å / Cross valid method: SHELLS OF RESOLUTION / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1485 1.52 %15 SHELLS
Rwork0.205 ---
obs0.205 97572 88.2 %-
Displacement parametersBiso mean: 31 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10560 0 192 686 11438
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.802
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.72
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.278
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.351 99 -
Rwork0.297 5066 -
obs--69.3 %
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_deg24.72
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.278

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