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

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Basic information

Entry
Database: PDB / ID: 6hlf
TitleX-ray structure of Lactobacillus brevis alcohol dehydrogenase mutant - K32A
ComponentsR-specific alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / short chain reductases/dehydrogenases / magnesium dependence / R-specific alcohol dehydrogenase
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
: / R-specific alcohol dehydrogenase
Similarity search - Component
Biological speciesLactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsHermann, J. / Nowotny, P. / Schneider, S. / Hekmat, D. / Weuster-Botz, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SPP 1934 Germany
CitationJournal: Cryst.Growth Des. / Year: 2019
Title: Rational Crystal Contact Engineering of Lactobacillus brevis Alcohol Dehydrogenase To Promote Technical Protein Crystallization
Authors: Nowotny, P. / Hermann, J. / Li, J. / Krautenbacher, A. / Klopfer, K. / Hekmat, D. / Weuster-Botz, D.
History
DepositionSep 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.0Oct 7, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / diffrn / entity / pdbx_audit_support / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conf / struct_conn / struct_site / struct_site_gen
Item: _diffrn.pdbx_serial_crystal_experiment / _entity.pdbx_number_of_molecules ..._diffrn.pdbx_serial_crystal_experiment / _entity.pdbx_number_of_molecules / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _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.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 / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.d_res_high / _refine_ls_shell.pdbx_total_number_of_bins_used / _software.version / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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
Description: Ligand identity / Details: Replaced a O (HOH) partially by Mg / Provider: author / Type: Coordinate replacement
Revision 2.1Jan 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

Downloads & links

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Assembly

Deposited unit
A: R-specific alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9204
Polymers27,8161
Non-polymers1043
Water5,459303
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)111,67916
Polymers111,2654
Non-polymers41412
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 area14650 Å2
ΔGint-103 kcal/mol
Surface area32180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.580, 81.780, 114.890
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-302-

MN

31A-303-

MG

41A-462-

HOH

51A-569-

HOH

61A-574-

HOH

71A-583-

HOH

81A-681-

HOH

91A-689-

HOH

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Components

#1: Protein R-specific alcohol dehydrogenase


Mass: 27816.270 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.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Protein solution (30 g LbADH L -1 , 20 mM HEPES/NaOH pH 7.0, 1 mM MgCl 2 and precipitation buffer (1 mM Tris/HCl pH 7.5, 50 mM MgCl 2 and 273 mM PEG 550 MME)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.968 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.55→45.97 Å / Num. obs: 38205 / % possible obs: 99.6 % / Redundancy: 9.1 % / Biso Wilson estimate: 23.28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08059 / Rpim(I) all: 0.02802 / Rrim(I) all: 0.08545 / Net I/σ(I): 17.07
Reflection shellResolution: 1.552→1.608 Å / Redundancy: 9.2 % / Rmerge(I) obs: 2.356 / Mean I/σ(I) obs: 0.74 / Num. unique obs: 3772 / CC1/2: 0.405 / Rpim(I) all: 0.8105 / Rrim(I) all: 2.494 / % possible all: 97.39

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6h07

6h07


Resolution: 1.55→45.97 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.052 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.079 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1965 1913 5 %RANDOM
Rwork0.172 ---
obs0.1732 36331 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.94 Å2 / Biso mean: 21.68 Å2 / Biso min: 13.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å2-0 Å2-0 Å2
2--2.38 Å20 Å2
3----1.2 Å2
Refinement stepCycle: final / Resolution: 1.55→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1867 0 3 303 2173
Biso mean--35.21 36.3 -
Num. residues----251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132058
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171905
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.6342803
X-RAY DIFFRACTIONr_angle_other_deg1.4581.5844427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0655280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.58423.88990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.115349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.291158
X-RAY DIFFRACTIONr_chiral_restr0.0710.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022558
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02442
LS refinement shellResolution: 1.55→1.589 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.702 130 -
Rwork0.724 2456 -
obs--92.46 %

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