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- PDB-6y1b: X-ray structure of Lactobacillus brevis alcohol dehydrogenase mut... -

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Basic information

Entry
Database: PDB / ID: 6y1b
TitleX-ray structure of Lactobacillus brevis alcohol dehydrogenase mutant K32A_Q126K
ComponentsR-specific alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / Nucleotide Binding Oxidoreductase Activity
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / R-specific alcohol dehydrogenase
Similarity search - Component
Biological speciesLactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 11, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr1_symmetry / _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_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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
A: R-specific alcohol dehydrogenase
B: R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8516
Polymers55,6352
Non-polymers2174
Water12,899716
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-21 kcal/mol
Surface area20340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.280, 82.030, 114.590
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
11A-1241-

HOH

21A-1417-

HOH

31B-491-

HOH

41B-589-

HOH

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Components

#1: Protein R-specific alcohol dehydrogenase


Mass: 27817.320 Da / Num. of mol.: 2 / Mutation: K32A, Q126K
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 716 / 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: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growTemperature: 293 K / Method: microbatch
Details: Protein solution (5 g/L LbADH , 20 mM HEPES/NaOH pH 7.0, 1 mM MgCl2 and precipitation buffer (1 mM Tris/HCl pH 7.0, 50 mM MgCl2 and 50 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: X06SA / Wavelength: 1.0000089622351 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0000089622351 Å / Relative weight: 1
ReflectionResolution: 1.4→47 Å / Num. obs: 102746 / % possible obs: 99.6 % / Redundancy: 6.17 % / CC1/2: 0.999 / Net I/σ(I): 16.34
Reflection shellResolution: 1.4→1.49 Å / Num. unique obs: 29422 / CC1/2: 0.764 / % possible all: 90.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSMar 15, 2019data reduction
XSCALEMar 15, 2019data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6h07

6h07


Resolution: 1.4→46.97 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.981 / SU B: 1.587 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.043
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1355 5134 5 %RANDOM
Rwork0.1051 ---
obs0.1066 97589 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 72.91 Å2 / Biso mean: 18.324 Å2 / Biso min: 9.31 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å20 Å2
2---0.12 Å20 Å2
3----0.9 Å2
Refinement stepCycle: final / Resolution: 1.4→46.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3734 0 13 716 4463
Biso mean--32.24 33.23 -
Num. residues----502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134047
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173779
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.6395499
X-RAY DIFFRACTIONr_angle_other_deg1.5691.5828807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3955548
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.09723.514185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.515704
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7531519
X-RAY DIFFRACTIONr_chiral_restr0.0820.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024714
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02811
X-RAY DIFFRACTIONr_rigid_bond_restr2.08637823
LS refinement shellResolution: 1.404→1.441 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 334 -
Rwork0.193 6346 -
all-6680 -
obs--87.93 %

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