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- PDB-6y10: X-ray structure of Lactobacillus brevis alcohol dehydrogenase mut... -

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Basic information

Entry
Database: PDB / ID: 6y10
TitleX-ray structure of Lactobacillus brevis alcohol dehydrogenase mutant Q126H
ComponentsR-specific alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / Nucleotide Binding Oxidoreductase Activity
Function / homology
Function and homology information


bile acid metabolic process / 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
R-specific alcohol dehydrogenase
Similarity search - Component
Biological speciesLactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 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: Crystals / Year: 2021
Title: Controlling Protein Crystallization by Free Energy Guided Design of Interactions at Crystal Contacts
Authors: Hermann, J. / Bischoff, D. / Grob, P. / Janowski, R. / Hekmat, D. / Niessing, D. / Zacharias, M. / Weuster-Botz, D.
History
DepositionFeb 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 2.0Sep 30, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / pdbx_distant_solvent_atoms / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_symm_contact / refine / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _entity.pdbx_number_of_molecules / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details
Description: Atomic clashes
Details: Replacement of an unrealistic placed MG atom by O (HOH)
Provider: author / Type: Coordinate replacement
Revision 2.1Jun 9, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.2Jan 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,47813
Polymers27,8841
Non-polymers59412
Water7,332407
1
A: R-specific alcohol dehydrogenase
hetero molecules

A: R-specific alcohol dehydrogenase
hetero molecules

A: R-specific alcohol dehydrogenase
hetero molecules

A: R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,91352
Polymers111,5384
Non-polymers2,37548
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area21380 Å2
ΔGint-139 kcal/mol
Surface area32400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.050, 80.570, 113.470
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-301-

MG

21A-311-

MG

31A-402-

HOH

41A-475-

HOH

51A-587-

HOH

61A-600-

HOH

71A-755-

HOH

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Components

#1: Protein R-specific alcohol dehydrogenase


Mass: 27884.389 Da / Num. of mol.: 1
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.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 293 K / Method: microbatch
Details: Protein solution (10 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 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: 0.966 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: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.22→46.01 Å / Num. obs: 75851 / % possible obs: 99.1 % / Redundancy: 6.96 % / CC1/2: 0.999 / Net I/σ(I): 13.49
Reflection shellResolution: 1.22→1.25 Å / Num. unique obs: 5601 / CC1/2: 0.709 / % possible all: 99.4

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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: 1.22→46.01 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.389 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1639 3793 5 %RANDOM
Rwork0.1378 ---
obs0.1391 72057 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 70.59 Å2 / Biso mean: 14.309 Å2 / Biso min: 6.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2---0.25 Å20 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 1.22→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 37 406 2315
Biso mean--32.53 33.97 -
Num. residues----251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132162
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172001
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.6422950
X-RAY DIFFRACTIONr_angle_other_deg1.5471.5824692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7055300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1932495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.10315377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.079158
X-RAY DIFFRACTIONr_chiral_restr0.0760.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022510
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02422
X-RAY DIFFRACTIONr_rigid_bond_restr1.12634156
LS refinement shellResolution: 1.22→1.252 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 280 -
Rwork0.349 5317 -
all-5597 -
obs--99.43 %

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