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- PDB-6y0s: X-ray structure of Lactobacillus brevis alcohol dehydrogenase mut... -

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Basic information

Entry
Database: PDB / ID: 6y0s
TitleX-ray structure of Lactobacillus brevis alcohol dehydrogenase mutant T102E
ComponentsR-specific alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / Nucleotide Binding Oxidoreductase Activity
Function / homologyShort-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / nucleotide binding / metal ion binding / R-specific alcohol dehydrogenase
Function and homology information
Biological speciesLactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsHermann, J. / Bischoff, D. / Janowski, R. / Niessing, D. / Grob, P. / Hekmat, D. / Weuster-Botz, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)WE2715/14-1 Germany
CitationJournal: Biotechnol J / Year: 2020
Title: Crystal Contact Engineering Enables Efficient Capture and Purification of an Oxidoreductase by Technical Crystallization.
Authors: Grob, P. / Huber, M. / Walla, B. / Hermann, J. / Janowski, R. / Niessing, D. / Hekmat, D. / Weuster-Botz, D.
History
DepositionFeb 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_symmetry
Revision 1.2Dec 16, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: R-specific alcohol dehydrogenase
BBB: R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,02411
Polymers55,8052
Non-polymers2199
Water13,908772
1
AAA: R-specific alcohol dehydrogenase
BBB: R-specific alcohol dehydrogenase
hetero molecules

AAA: R-specific alcohol dehydrogenase
BBB: R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,04722
Polymers111,6104
Non-polymers43718
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15980 Å2
ΔGint-225 kcal/mol
Surface area32550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.620, 81.150, 115.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11AAA-607-

HOH

21BBB-622-

HOH

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Components

#1: Protein R-specific alcohol dehydrogenase


Mass: 27902.381 Da / Num. of mol.: 2 / Mutation: T102E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis (bacteria) / Gene: radh / Production host: Escherichia coli (E. coli) / References: UniProt: Q84EX5
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 772 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein solution ( 10 g/L LbADH , 20 mM HEPES/NaOH pH 7.0, 1 mM MgCl2 and precipitation buffer (100 mM Tris/HCl pH 7.0, 50 mM MgCl2 and 100 g/L PEG 550 MME)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.44→47.068 Å / Num. obs: 94960 / % possible obs: 99.7 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rrim(I) all: 0.109 / Net I/σ(I): 16.16
Reflection shellResolution: 1.44→1.47 Å / Redundancy: 13 % / Mean I/σ(I) obs: 2.06 / Num. unique obs: 6977 / CC1/2: 0.683 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSMar 15, 2019data reduction
XSCALEMar 15, 2019data scaling
PHASES2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6h07

6h07


Resolution: 1.44→47.068 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.156 / WRfactor Rwork: 0.12 / SU B: 2.616 / SU ML: 0.043 / Average fsc free: 0.9319 / Average fsc work: 0.9444 / Cross valid method: FREE R-VALUE / ESU R: 0.06 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1684 4748 5 %
Rwork0.1297 90211 -
all0.132 --
obs-94959 99.633 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.333 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å20 Å2-0 Å2
2--1.027 Å20 Å2
3---0.523 Å2
Refinement stepCycle: LAST / Resolution: 1.44→47.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3746 0 9 772 4527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134045
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173744
X-RAY DIFFRACTIONr_angle_refined_deg1.281.6375503
X-RAY DIFFRACTIONr_angle_other_deg1.4111.5818740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4745551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.00924.076184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.37915702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9281516
X-RAY DIFFRACTIONr_chiral_restr0.0630.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024726
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02802
X-RAY DIFFRACTIONr_nbd_refined0.2270.2852
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.23600
X-RAY DIFFRACTIONr_nbtor_refined0.1560.22018
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21574
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2548
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1630.223
X-RAY DIFFRACTIONr_nbd_other0.1840.2101
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1660.277
X-RAY DIFFRACTIONr_mcbond_it1.0431.4442127
X-RAY DIFFRACTIONr_mcbond_other1.0431.4442126
X-RAY DIFFRACTIONr_mcangle_it1.3632.1732694
X-RAY DIFFRACTIONr_mcangle_other1.3622.1732695
X-RAY DIFFRACTIONr_scbond_it1.3841.671918
X-RAY DIFFRACTIONr_scbond_other1.3851.6711915
X-RAY DIFFRACTIONr_scangle_it1.6972.4262805
X-RAY DIFFRACTIONr_scangle_other1.6972.4262804
X-RAY DIFFRACTIONr_lrange_it3.56120.424923
X-RAY DIFFRACTIONr_lrange_other2.77218.7444660
X-RAY DIFFRACTIONr_rigid_bond_restr0.76937786
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.44-1.4770.283480.26166200.26269790.8170.82799.84240.245
1.477-1.5180.2453380.20564170.20767810.8820.89199.61660.189
1.518-1.5620.2153310.18362900.18466360.9090.91999.7740.162
1.562-1.610.2233180.15760550.16163740.9190.93899.98430.137
1.61-1.6630.2033120.14559240.14862370.9310.94999.9840.125
1.663-1.7210.1813010.12957230.13160250.9490.96199.98340.107
1.721-1.7860.1752920.11855420.12158350.9570.96699.98290.097
1.786-1.8580.1672810.11453440.11756280.9590.96899.94670.093
1.858-1.9410.252590.19749120.253460.8230.88696.72650.164
1.941-2.0360.162580.11849120.1251740.9550.96299.92270.1
2.036-2.1450.1622460.10646690.10849240.9690.98199.81720.092
2.145-2.2750.1482290.11543440.11746400.9660.97398.5560.098
2.275-2.4320.1472190.09441720.09644050.9730.98199.68220.083
2.432-2.6260.1432050.09438960.09641030.9780.98499.95130.086
2.626-2.8760.1351890.135880.10237790.9790.98299.94710.095
2.876-3.2140.1551730.11332890.11534630.9710.9899.97110.113
3.214-3.7080.1591530.12629050.12830600.9750.9899.93460.131
3.708-4.5350.1191300.11524690.11526020.9850.98399.88470.127
4.535-6.3830.1461040.13919680.13920750.9820.98599.85540.159
6.383-47.0680.228620.17311730.17612400.950.96499.59680.214

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