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- PDB-1ped: BACTERIAL SECONDARY ALCOHOL DEHYDROGENASE (APO-FORM) -

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Basic information

Entry
Database: PDB / ID: 1ped
TitleBACTERIAL SECONDARY ALCOHOL DEHYDROGENASE (APO-FORM)
ComponentsNADP-DEPENDENT ALCOHOL DEHYDROGENASE
KeywordsOXIDOREDUCTASE / THERMOSTABLE / 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 / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain ...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 / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / 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-dependent isopropanol dehydrogenase
Similarity search - Component
Biological speciesClostridium beijerinckii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.15 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
DepositionDec 28, 1995Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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

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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)151,3138
Polymers151,0524
Non-polymers2624
Water10,052558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14230 Å2
ΔGint-143 kcal/mol
Surface area44130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.400, 102.260, 193.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(-0.999998, -0.000661, 0.001893), (0.001896, -0.00411, 0.99999), (-0.000654, 0.999991, 0.004111)0.70556, -71.31985, 70.89779
2given(-0.524097, 0.585527, -0.61845), (0.607478, -0.251938, -0.753325), (-0.596903, -0.77051, -0.223654)45.01479, 61.79718, 95.68276
3given(0.523831, -0.612314, 0.592177), (-0.601026, -0.758314, -0.252443), (0.60363, -0.223676, -0.765245)-41.79111, 26.71804, 133.8252

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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: APO-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 32 %
Crystal growpH: 7.5 / Details: SEE REFERENCE 1., pH 7.5
Crystal grow
*PLUS
Temperature: 293 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
250 mMTris-HCl1drop
350 mM1dropNaCl
40.1 mMdithiothreitol1drop
50.05 M1dropZnCl2
616 %PEG40001reservoir
750 mM1reservoirNaCl
850 mMTris-HCl1reservoir

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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: 2.15→50 Å / Num. obs: 69617 / % possible obs: 79 % / Observed criterion σ(I): 0 / Redundancy: 2.48 % / Biso Wilson estimate: 34.3 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 28.5
Reflection shellResolution: 2.15→2.18 Å / Redundancy: 1.53 % / Mean I/σ(I) obs: 4.68 / Rsym value: 0.267 / % possible all: 51.3
Reflection shell
*PLUS
% possible obs: 51.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.15→50 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1545 2.22 %15 RESOLUTION SHELLS
Rwork0.215 ---
obs0.215 69617 79 %-
Displacement parametersBiso mean: 43.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10560 0 4 558 11122
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.524
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.96
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.054
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
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDWeight Biso Weight position
11NCS RESTRAINS ON EACH MONOMERX-RAY DIFFRACTION1100
22X-RAY DIFFRACTION1100
33X-RAY DIFFRACTION1100
44X-RAY DIFFRACTION1100
LS refinement shellResolution: 2.15→2.2 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.364 103 -
Rwork0.313 3620 -
obs--51.3 %
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_deg22.96
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.054

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