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- PDB-3fpl: Chimera of alcohol dehydrogenase by exchange of the cofactor bind... -

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Basic information

Entry
Database: PDB / ID: 3fpl
TitleChimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-295 of C. beijerinckii ADH by T. brockii ADH
ComponentsNADP-dependent alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / oxydoreductase / bacterial alcohol dehydrogenase / domain exchange / chimera / Metal-binding / 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
CACODYLATE ION / TRIETHYLENE GLYCOL / NADP-dependent isopropanol dehydrogenase / NADP-dependent isopropanol dehydrogenase
Similarity search - Component
Biological speciesClostridium beijerinckii (bacteria)
Thermoanaerobacter brockii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsFelix, F. / Goihberg, E. / Shimon, L. / Burstein, Y.
CitationJournal: Biochemistry / Year: 2010
Title: Biochemical and structural properties of chimeras constructed by exchange of cofactor-binding domains in alcohol dehydrogenases from thermophilic and mesophilic microorganisms
Authors: Goihberg, E. / Peretz, M. / Tel-Or, S. / Dym, O. / Shimon, L. / Frolow, F. / Burstein, Y.
History
DepositionJan 5, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1327
Polymers37,6471
Non-polymers4866
Water7,422412
1
A: NADP-dependent alcohol dehydrogenase
hetero molecules

A: NADP-dependent alcohol dehydrogenase
hetero molecules

A: NADP-dependent alcohol dehydrogenase
hetero molecules

A: NADP-dependent alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,52928
Polymers150,5874
Non-polymers1,94224
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area20280 Å2
ΔGint-313 kcal/mol
Surface area43580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.477, 129.477, 129.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NADP-dependent alcohol dehydrogenase / CbADH


Mass: 37646.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 153-295 inserted from alcohol dehydrogenase of ENTAMOEBA HISTOLOTICA
Source: (gene. exp.) Clostridium beijerinckii (bacteria), (gene. exp.) Thermoanaerobacter brockii (bacteria)
Gene: ADH1, ADH1 / Plasmid: BS-P58 / Production host: Escherichia coli (E. coli) / Strain (production host): TG-I
References: UniProt: P25984, UniProt: P14941, alcohol dehydrogenase (NADP+)

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Non-polymers , 6 types, 418 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 298 K / pH: 5.6
Details: Single crystals of apo-22(CTC) were obtained by the microbatch method under oil at 18 C, using the IMPAX 1-5 robot. The apo-22(CTC) (10mg/mL) was crystallized in a mixture containing 100mM ...Details: Single crystals of apo-22(CTC) were obtained by the microbatch method under oil at 18 C, using the IMPAX 1-5 robot. The apo-22(CTC) (10mg/mL) was crystallized in a mixture containing 100mM ammonium acetate, 15% (w/v) PEG 4000, 25mM NaCl, 50mM DTT, 25mM ZnCl2 and 50mM tri-citrate dihydrate (pH sodium 5.6), Microbatch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→91.67 Å / Num. obs: 28452 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 30.2
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 12 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2004 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.41 / Cor.coef. Fo:Fc: 0.536
Highest resolutionLowest resolution
Rotation4 Å19.98 Å
Translation4 Å19.98 Å

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
ProDCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PED

1ped


Resolution: 1.9→19.98 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.178 / WRfactor Rwork: 0.128 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.922 / SU B: 4.521 / SU ML: 0.072 / SU R Cruickshank DPI: 0.111 / SU Rfree: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.172 1437 5.1 %RANDOM
Rwork0.122 ---
obs0.125 28452 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 85.83 Å2 / Biso mean: 24.753 Å2 / Biso min: 10.39 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2635 0 22 412 3069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222742
X-RAY DIFFRACTIONr_bond_other_d0.0020.021850
X-RAY DIFFRACTIONr_angle_refined_deg1.5531.9733715
X-RAY DIFFRACTIONr_angle_other_deg0.99834543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8635362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60724.34106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.59315470
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5571514
X-RAY DIFFRACTIONr_chiral_restr0.0980.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023064
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02522
X-RAY DIFFRACTIONr_nbd_refined0.2160.2544
X-RAY DIFFRACTIONr_nbd_other0.2020.22036
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21322
X-RAY DIFFRACTIONr_nbtor_other0.0870.21407
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2310.2290
X-RAY DIFFRACTIONr_metal_ion_refined0.0290.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3760.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.243
X-RAY DIFFRACTIONr_mcbond_it2.14232245
X-RAY DIFFRACTIONr_mcbond_other0.5673734
X-RAY DIFFRACTIONr_mcangle_it2.54252813
X-RAY DIFFRACTIONr_scbond_it4.49771138
X-RAY DIFFRACTIONr_scangle_it5.57910897
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 115 -
Rwork0.167 1929 -
all-2044 -
obs--99.08 %

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