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- PDB-6h1m: Neutron structure of Lactobacillus brevis alcohol dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 6h1m
TitleNeutron structure of Lactobacillus brevis alcohol dehydrogenase
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 speciesLevilactobacillus brevis (bacteria)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHermann, J. / Nowotny, P. / Schrader, T.E. / Biggel, P. / Hekmat, D. / Weuster-Botz, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSPP 1934 Germany
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Neutron and X-ray crystal structures of Lactobacillus brevis alcohol dehydrogenase reveal new insights into hydrogen-bonding pathways.
Authors: Hermann, J. / Nowotny, P. / Schrader, T.E. / Biggel, P. / Hekmat, D. / Weuster-Botz, D.
History
DepositionJul 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 2.0Jan 24, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_alt_id / _atom_site.label_atom_id / _atom_site.occupancy / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_strain / _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 / _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

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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)26,7353
Polymers26,6561
Non-polymers792
Water1,63991
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)106,94112
Polymers106,6244
Non-polymers3178
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 area14920 Å2
ΔGint-122 kcal/mol
Surface area32880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.508, 84.572, 115.419
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-301-

MG

21A-302-

MN

31A-465-

HOH

41A-472-

HOH

51A-484-

HOH

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Components

#1: Protein R-specific alcohol dehydrogenase


Mass: 26656.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Levilactobacillus brevis (bacteria) / Gene: radh / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q84EX5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 550 MME, Magnesium chloride, HEPES

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Data collection

DiffractionMean temperature: 293.15 K / Serial crystal experiment: N
Diffraction sourceSource: NUCLEAR REACTOR / Site: FRM II / Beamline: BIODIFF / Wavelength: 2.675 Å
DetectorType: MAATEL BIODIFF / Detector: IMAGE PLATE / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 2.675 Å / Relative weight: 1
ReflectionResolution: 2.15→21.76 Å / Num. obs: 14121 / % possible obs: 91.56 % / Redundancy: 2.6 % / Biso Wilson estimate: 14.47 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.111 / Rrim(I) all: 0.192 / Net I/σ(I): 5.14
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.24 / Num. unique obs: 995 / CC1/2: 0.61 / Rpim(I) all: 0.282 / Rrim(I) all: 0.466 / % possible all: 79.01

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000v705bdata reduction
Coot0.8.9model building
HKL-2000v705bdata scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H07

6h07


Resolution: 2.15→21.759 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2493 1412 10 %
Rwork0.2177 --
obs0.221 14119 91.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0614219
NEUTRON DIFFRACTIONf_angle_d2.8287455
NEUTRON DIFFRACTIONf_dihedral_angle_d19.6651124
NEUTRON DIFFRACTIONf_chiral_restr0.06293
NEUTRON DIFFRACTIONf_plane_restr0.006780
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1498-2.22660.28881200.26911081NEUTRON DIFFRACTION79
2.2266-2.31560.30871190.27081066NEUTRON DIFFRACTION79
2.3156-2.42090.30931290.26251163NEUTRON DIFFRACTION85
2.4209-2.54830.27591380.24911246NEUTRON DIFFRACTION91
2.5483-2.70770.32321430.24311280NEUTRON DIFFRACTION93
2.7077-2.91630.27491450.23121309NEUTRON DIFFRACTION95
2.9163-3.2090.24341510.21891355NEUTRON DIFFRACTION97
3.209-3.67140.19241520.1961376NEUTRON DIFFRACTION98
3.6714-4.61830.18431550.16451391NEUTRON DIFFRACTION99
4.6183-21.75980.22131600.18081440NEUTRON DIFFRACTION98

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