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- PDB-1jvi: THE 2.2 ANGSTROM RESOLUTION STRUCTURE OF BACILLUS SUBTILIS LUXS/R... -

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Basic information

Entry
Database: PDB / ID: 1jvi
TitleTHE 2.2 ANGSTROM RESOLUTION STRUCTURE OF BACILLUS SUBTILIS LUXS/RIBOSILHOMOCYSTEINE COMPLEX
ComponentsAutoinducer-2 production protein luxS
KeywordsSIGNALING PROTEIN / AUTOINDUCER SYNTHESIS
Function / homology
Function and homology information


S-ribosylhomocysteine lyase / S-ribosylhomocysteine lyase activity / quorum sensing / iron ion binding
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 / Chem-RHC / S-ribosylhomocysteine lyase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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. / Hartley, A. / Horsburg, M.J. / Rice, D.W.
History
DepositionAug 30, 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 2.0Jul 29, 2020Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.4Apr 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)18,3545
Polymers17,7901
Non-polymers5644
Water1,45981
1
A: Autoinducer-2 production protein luxS
hetero molecules

A: Autoinducer-2 production protein luxS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,70810
Polymers35,5802
Non-polymers1,1288
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area4440 Å2
ΔGint-63 kcal/mol
Surface area12250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.095, 62.095, 150.051
Angle α, β, γ (deg.)90, 90, 120
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

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Protein / Sugars , 2 types, 2 molecules A

#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) / Gene: LUXS / Plasmid: PSKD1 / Production host: Escherichia coli (E. coli) / Strain (production host): TUNER (DE3) PLACI / References: UniProt: O34667
#4: Sugar ChemComp-RHC / (2S)-2-amino-4-[[(2S,3S,4R,5R)-3,4,5-trihydroxyoxolan-2-yl]methylsulfanyl]butanoic acid / 5-(3-AMINO-4,4-DIHYROXY-BUTYLSULFANYLMETHYL)-TETRAHYDRO-FURAN-2,3,4-TRIOL


Type: D-saccharide, beta linking / Mass: 267.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H17NO6S

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Non-polymers , 4 types, 84 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.55 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 1.8 - 2.4M AMMONIUM SULPHATE, 0.1M TRIS-HCL, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
pH: 8
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 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 8944 / Num. obs: 8944 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.63 % / Biso Wilson estimate: 36.49 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.1
Reflection shellResolution: 2.2→2.25 Å / Rmerge(I) obs: 0.36 / Num. unique all: 553 / % possible all: 92.5
Reflection
*PLUS
Num. measured all: 24877
Reflection shell
*PLUS
Num. unique obs: 339 / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.3

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Processing

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

1j98


Resolution: 2.2→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2419 491 -RANDOM
Rwork0.1739 ---
all-8850 --
obs-8359 96.4 %-
Displacement parametersBiso mean: 37.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 31 81 1337
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0107
X-RAY DIFFRACTIONc_angle_deg1.5121
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.955
X-RAY DIFFRACTIONc_mcbond_it5.66
X-RAY DIFFRACTIONc_mcangle_it8.9
X-RAY DIFFRACTIONc_scbond_it6.55
X-RAY DIFFRACTIONc_scangle_it10.83
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.2-2.340.313740.263X-RAY DIFFRACTION1391
2.34-2.510.321820.238X-RAY DIFFRACTION1425
2.51-2.760.382730.223X-RAY DIFFRACTION1452
2.76-3.150.247780.177X-RAY DIFFRACTION1481
3.15-3.930.199860.151X-RAY DIFFRACTION1529
3.93-100.212980.142X-RAY DIFFRACTION1572
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 10 Å / σ(F): 1 / Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.955
LS refinement shell
*PLUS
Lowest resolution: 10 Å / Rfactor Rfree: 0.212 / Rfactor Rwork: 0.142

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