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- PDB-1j98: The 1.2 Angstrom Structure of Bacillus subtilis LuxS -

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Basic information

Entry
Database: PDB / ID: 1j98
TitleThe 1.2 Angstrom Structure of Bacillus subtilis LuxS
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
S-ribosylhomocysteine lyase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.2 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: Acta Crystallogr.,Sect.D / Year: 2001
Title: Cloning, 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
DepositionMay 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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_asym_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_asym_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AUTOINDUCER-2 PRODUCTION PROTEIN LUXS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8562
Polymers17,7901
Non-polymers651
Water3,909217
1
A: AUTOINDUCER-2 PRODUCTION PROTEIN LUXS
hetero molecules

A: AUTOINDUCER-2 PRODUCTION PROTEIN LUXS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7114
Polymers35,5802
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area4000 Å2
ΔGint-93 kcal/mol
Surface area12750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.780, 62.780, 149.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe second part of the biological assembly is generated by the two fold axis: x, x-y, 5/6-z.

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Components

#1: Protein AUTOINDUCER-2 PRODUCTION PROTEIN LUXS / 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) / Production host: Escherichia coli (E. coli) / References: UniProt: O34667
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.5 Å3/Da / Density % sol: 39.56 %
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: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 9, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.2→10 Å / Num. all: 53328 / Num. obs: 53328 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 32.9
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1714 / % possible all: 63.3
Reflection
*PLUS
Num. measured all: 288300
Reflection shell
*PLUS
% possible obs: 63.6 %

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.2→10 Å / SU B: 1.056 / SU ML: 0.025 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.031 / ESU R Free: 0.031 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.146 2714 5.1 %RANDOM
Rwork0.126 ---
all0.127 50614 --
obs0.127 50614 96.5 %-
Displacement parametersBiso mean: 16.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20.39 Å20 Å2
2--0.78 Å20 Å2
3----1.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.031 Å0.031 Å
Luzzati sigma a-0.025 Å
Refinement stepCycle: LAST / Resolution: 1.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 1 217 1443
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d1.563
X-RAY DIFFRACTIONp_chiral_restr0.11
X-RAY DIFFRACTIONp_mcbond_it4.245
X-RAY DIFFRACTIONp_mcangle_it6.065
X-RAY DIFFRACTIONp_scbond_it9.269
X-RAY DIFFRACTIONp_scangle_it11.793
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.2 Å / σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.126
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.8 Å2

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