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- PDB-4fr2: Alcohol dehydrogenase from Oenococcus oeni -

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Basic information

Entry
Database: PDB / ID: 4fr2
TitleAlcohol dehydrogenase from Oenococcus oeni
Components1,3-propanediol dehydrogenase
KeywordsOxidoreductase / Metal Binding Protein / Rossmann fold
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity / metal ion binding
Similarity search - Function
Iron-type alcohol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold ...Iron-type alcohol dehydrogenase-like / Iron-containing alcohol dehydrogenases signature 1. / Alcohol dehydrogenase, iron-type, conserved site / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA / Iron-containing alcohol dehydrogenase / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / 1,3-propanediol dehydrogenase
Similarity search - Component
Biological speciesOenococcus oeni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsFodor, K. / Skander, E. / Wilmanns, M.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2013
Title: Structural and biochemical characterisation of a NAD(+)-dependent alcohol dehydrogenase from Oenococcus oeni as a new model molecule for industrial biotechnology applications.
Authors: Elleuche, S. / Fodor, K. / Klippel, B. / von der Heyde, A. / Wilmanns, M. / Antranikian, G.
History
DepositionJun 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Oct 9, 2013Group: Database references
Revision 1.4Sep 13, 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 / 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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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

Downloads & links

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Assembly

Deposited unit
A: 1,3-propanediol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5342
Polymers43,4751
Non-polymers591
Water00
1
A: 1,3-propanediol dehydrogenase
hetero molecules

A: 1,3-propanediol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0684
Polymers86,9512
Non-polymers1172
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2910 Å2
ΔGint-39 kcal/mol
Surface area27750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.825, 88.825, 151.028
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein 1,3-propanediol dehydrogenase


Mass: 43475.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oenococcus oeni (bacteria) / Gene: dhaT, OENOO_49030 / Production host: Escherichia coli (E. coli) / References: UniProt: A0NIJ1
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni

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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: 3.43 Å3/Da / Density % sol: 64.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES (pH 6.5), 16 % [w/w] PEG20000, 10mM CaCl2 in the drops, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.2→76.56 Å / Num. obs: 10505 / % possible obs: 59 %

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BFJ Chain A

3bfj


Resolution: 3.2→76.56 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.88 / SU B: 29.009 / SU ML: 0.494 / Cross valid method: THROUGHOUT / σ(F): 1.9 / ESU R Free: 0.565 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33406 498 4.8 %RANDOM
Rwork0.27881 ---
obs0.28131 9935 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.065 Å2
Baniso -1Baniso -2Baniso -3
1-3.93 Å2-0 Å2-0 Å2
2--3.93 Å20 Å2
3----7.86 Å2
Refinement stepCycle: LAST / Resolution: 3.2→76.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2668 0 1 0 2669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212712
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.9663707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0455382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91225.91898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.57315371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.187157
X-RAY DIFFRACTIONr_chiral_restr0.0810.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212083
X-RAY DIFFRACTIONr_mcbond_it0.3911.51902
X-RAY DIFFRACTIONr_mcangle_it0.72622977
X-RAY DIFFRACTIONr_scbond_it0.6363810
X-RAY DIFFRACTIONr_scangle_it1.1714.5730
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.498 46 -
Rwork0.403 716 -
obs--100 %

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