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

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Basic information

Entry
Database: PDB / ID: 3fpc
TitleChimera of alcohol dehydrogenase by exchange of the cofactor binding domain res 153-294 of T. brockii ADH by E. histolytica 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 / cytoplasm
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 / IMIDAZOLE / NITRATE ION / OXYGEN MOLECULE / NADP-dependent isopropanol dehydrogenase / NADP-dependent isopropanol dehydrogenase
Similarity search - Component
Biological speciesThermoanaerobacter brockii (bacteria)
Entamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 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
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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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_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)154,17032
Polymers152,2204
Non-polymers1,95028
Water35,8141988
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20640 Å2
ΔGint-178 kcal/mol
Surface area43380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.742, 82.429, 118.249
Angle α, β, γ (deg.)90.000, 99.890, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
NADP-dependent alcohol dehydrogenase


Mass: 38055.051 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Residues 153-294 inserted from alcohol dehydrogenase of ENTAMOEBA HISTOLOTICA
Source: (gene. exp.) Thermoanaerobacter brockii (bacteria), (gene. exp.) Entamoeba histolytica (eukaryote)
Gene: ADH1, ADH1 / Plasmid: BS-P58 / Production host: Escherichia coli (E. coli) / Strain (production host): TG-I
References: UniProt: P14941, UniProt: P35630, alcohol dehydrogenase (NADP+)

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Non-polymers , 8 types, 2016 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#7: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1988 / 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: 2.52 Å3/Da / Density % sol: 51.1 % / Mosaicity: 0.269 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8mg/mL protein [25mM Tris-HCl, 50mM NaCl, 0.1mM DTT, 50mM ZnCl2 (pH=7.5)] was mixed with 0.001 ml of reservoir solution [16% (w/v) PEG 8000, 200mM magnesium acetate tetrahydrate, 100mM ...Details: 8mg/mL protein [25mM Tris-HCl, 50mM NaCl, 0.1mM DTT, 50mM ZnCl2 (pH=7.5)] was mixed with 0.001 ml of reservoir solution [16% (w/v) PEG 8000, 200mM magnesium acetate tetrahydrate, 100mM Cacodylate buffer (pH 6.5)], vapor diffusion, hanging drop, 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: 1.4→50 Å / Num. all: 294442 / Num. obs: 294442 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.075 / Χ2: 1.656 / Net I/σ(I): 20.143
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 1.4 / Num. unique all: 13706 / Χ2: 1.27 / % possible all: 93

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.409 / Cor.coef. Fo:Fc: 0.552
Highest resolutionLowest resolution
Rotation4 Å48.77 Å
Translation4 Å48.77 Å

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Processing

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

1kev


Resolution: 1.4→48.77 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.154 / WRfactor Rwork: 0.116 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.93 / SU B: 1.708 / SU ML: 0.03 / SU R Cruickshank DPI: 0.048 / SU Rfree: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.155 14820 5.1 %RANDOM
Rwork0.116 ---
all0.118 283136 --
obs0.118 293136 99.14 %-
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: 498.96 Å2 / Biso mean: 15.204 Å2 / Biso min: 2.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å2-0.5 Å2
2---0.23 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.4→48.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10675 0 97 1988 12760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02211332
X-RAY DIFFRACTIONr_bond_other_d0.0010.027776
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.9615343
X-RAY DIFFRACTIONr_angle_other_deg0.991319046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61851494
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02123.996468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.914151941
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.241559
X-RAY DIFFRACTIONr_chiral_restr0.1030.21678
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212742
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022235
X-RAY DIFFRACTIONr_nbd_refined0.2180.22317
X-RAY DIFFRACTIONr_nbd_other0.2060.28673
X-RAY DIFFRACTIONr_nbtor_refined0.1760.25431
X-RAY DIFFRACTIONr_nbtor_other0.0860.25914
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.21575
X-RAY DIFFRACTIONr_metal_ion_refined0.1120.213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2330.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.256
X-RAY DIFFRACTIONr_mcbond_it2.40537109
X-RAY DIFFRACTIONr_mcbond_other1.26932972
X-RAY DIFFRACTIONr_mcangle_it3.311511468
X-RAY DIFFRACTIONr_scbond_it4.38774314
X-RAY DIFFRACTIONr_scangle_it6.226103841
X-RAY DIFFRACTIONr_rigid_bond_restr1.784319731
X-RAY DIFFRACTIONr_sphericity_free6.79531996
X-RAY DIFFRACTIONr_sphericity_bonded3.41318838
LS refinement shellResolution: 1.4→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 940 -
Rwork0.221 19107 -
all-20047 -
obs--92.17 %

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