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- PDB-1jqw: THE 2.3 ANGSTROM RESOLUTION STRUCTURE OF BACILLUS SUBTILIS LUXS/H... -

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Basic information

Entry
Database: PDB / ID: 1jqw
TitleTHE 2.3 ANGSTROM RESOLUTION STRUCTURE OF BACILLUS SUBTILIS LUXS/HOMOCYSTEINE COMPLEX
ComponentsAutoinducer-2 production protein luxS
KeywordsSIGNALING PROTEIN / AUTOINDUCER SYNTHESIS
Function / homology
Function and homology information


S-ribosylhomocysteine lyase / S-ribosylhomocysteine lyase activity / L-methionine salvage from S-adenosylmethionine / quorum sensing / iron ion binding / cytosol
Similarity search - Function
S-ribosylhomocysteinase (LuxS) / S-ribosylhomocysteinase (LuxS) / S-ribosylhomocysteinase (LuxS) superfamily / S-Ribosylhomocysteinase (LuxS) / Metalloenzyme, LuxS/M16 peptidase-like / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-AMINO-4-MERCAPTO-BUTYRIC ACID / S-ribosylhomocysteine lyase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRuzheinikov, S.N. / Das, S.K. / Sedelnikova, S.E. / Hartley, A. / Foster, S.J. / Horsburgh, M.J. / Cox, A.G. / McCleod, C.W. / Mekhalfia, A. / Blackburn, G.M. ...Ruzheinikov, S.N. / Das, S.K. / Sedelnikova, S.E. / Hartley, A. / Foster, S.J. / Horsburgh, M.J. / Cox, A.G. / McCleod, C.W. / Mekhalfia, A. / Blackburn, G.M. / Rice, D.W. / Baker, P.J.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: The 1.2 A structure of a novel quorum-sensing protein, Bacillus subtilis LuxS
Authors: Ruzheinikov, S.N. / Das, S.K. / Sedelnikova, S.E. / Hartley, A. / Foster, S.J. / Horsburgh, M.J. / Cox, A.G. / McCleod, C.W. / Mekhalfia, A. / Blackburn, G.M. / Rice, D.W. / Baker, P.J.
#1: Journal: TO BE PUBLISHED
Title: PURIFICATION, CRYSTALLIZATION AND PRELIMINARY CRYSTALLOGRAPHIC ANALYSIS OF BACILLUS SUBTILIS LUXS
Authors: Das, S.K. / Sedelnikova, S.E. / Baker, P.J. / Ruzheinikov, S.N. / Foster, S.J. / Hartley, A. / Horsburgh, M.J. / Rice, D.W.
History
DepositionAug 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Apr 3, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Autoinducer-2 production protein luxS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2615
Polymers17,7901
Non-polymers4714
Water95553
1
A: Autoinducer-2 production protein luxS
hetero molecules

A: Autoinducer-2 production protein luxS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,52210
Polymers35,5802
Non-polymers9428
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area3660 Å2
ΔGint-82 kcal/mol
Surface area12510 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.202, 61.202, 150.030
Angle α, β, γ (deg.)90.000, 90.000, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the matrix: BIOMT1 2 0.500000 0.866025 0.000000 -31.39000 BIOMT2 2 0.866025 -0.500000 0.000000 54.36907 BIOMT3 2 0.000000 0.000000 -1.000000 -24.93000

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Components

#1: Protein Autoinducer-2 production protein luxS / S-ribosylhomocysteine lyase / AI-2 synthesis protein


Mass: 17790.219 Da / Num. of mol.: 1 / Mutation: P96T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: luxS / Plasmid: pSKD1 / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner (DE3) pLacI / References: UniProt: O34667, S-ribosylhomocysteine lyase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H9NO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.8 - 2.4M AMMONIUM SULPHATE, 0.1M TRIS-HCL, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8-2.2 Mammonium sulfate1reservoir
20.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 7264 / Num. obs: 7264 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.36 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 20.8
Reflection shellResolution: 2.3→2.35 Å / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 3.35 / Num. unique all: 494 / % possible all: 94.5
Reflection
*PLUS
Num. measured all: 38530 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 94.5 % / Num. unique obs: 185 / Rmerge(I) obs: 0.501

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J98

1j98


Resolution: 2.3→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 395 -RANDOM
Rwork0.175 ---
obs-7180 91.6 %-
Displacement parametersBiso mean: 44.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1191 0 25 53 1269
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.51
X-RAY DIFFRACTIONc_bond_d0.0109
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it6.39
X-RAY DIFFRACTIONc_mcangle_it8.65
X-RAY DIFFRACTIONc_scbond_it7.8
X-RAY DIFFRACTIONc_scangle_it10.64
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 10 Å / σ(F): 1 / Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93
X-RAY DIFFRACTIONc_mcbond_it6.39
X-RAY DIFFRACTIONc_scbond_it7.8
X-RAY DIFFRACTIONc_mcangle_it8.65
X-RAY DIFFRACTIONc_scangle_it10.64

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