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- PDB-1ie0: CRYSTAL STRUCTURE OF LUXS -

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Basic information

Entry
Database: PDB / ID: 1ie0
TitleCRYSTAL STRUCTURE OF LUXS
ComponentsAUTOINDUCER-2 PRODUCTION PROTEIN LUXS
KeywordsSTRUCTURAL GENOMICS / four stranded antiparallel beta sheet / cysteine-sulfonic acid
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
S-ribosylhomocysteine lyase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.6 Å
AuthorsHilgers, M.T. / Ludwig, M.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Crystal structure of the quorum-sensing protein LuxS reveals a catalytic metal site.
Authors: Hilgers, M.T. / Ludwig, M.L.
History
DepositionApr 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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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)17,9443
Polymers17,7861
Non-polymers1582
Water3,369187
1
A: AUTOINDUCER-2 PRODUCTION PROTEIN LUXS
hetero molecules

A: AUTOINDUCER-2 PRODUCTION PROTEIN LUXS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8876
Polymers35,5722
Non-polymers3154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area4930 Å2
ΔGint-97 kcal/mol
Surface area12360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.732, 62.732, 150.140
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 (dimer) is generated by the crystallographic two fold.

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Components

#1: Protein AUTOINDUCER-2 PRODUCTION PROTEIN LUXS / AI-2 SYNTHESIS PROTEIN


Mass: 17786.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: LUXS / Plasmid: PET29 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O34667
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.4 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Ammonium sulfate, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 mg/mlprotein1drop
220 mMTris1drop
32 mMtri(carboxyethyl)phosphine1drop
41.8 Mammonium sulfate1reservoir
5100 mMTris1reservoir

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 22, 1999 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 23431 / Num. obs: 23431 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 30.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 10 % / Rmerge(I) obs: 0.357 / % possible all: 92.8
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 98 % / Num. measured all: 413208
Reflection shell
*PLUS
% possible obs: 92.8 %

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.6→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: MEASURED REFLECTIONS WITH |F| = 0 NOT USED IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2203 10 %RANDOM
Rwork0.174 ---
all0.174 21965 --
obs0.174 21965 91.8 %-
Solvent computationBsol: 63.204 Å2 / ksol: 0.404425 e/Å3
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.936 Å2-2.279 Å20 Å2
2---1.936 Å20 Å2
3---3.872 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1237 0 7 187 1431
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.01561
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.81733
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it3.031.5
X-RAY DIFFRACTIONo_mcangle_it5.092
X-RAY DIFFRACTIONo_scbond_it3.712
X-RAY DIFFRACTIONo_scangle_it6.522.5
LS refinement shellResolution: 1.6→1.67 Å /
RfactorNum. reflection
Rfree0.381 134
Rwork0.3365 1290
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2gol.pargol.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5cyo.parcyo.top
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Rfactor Rfree: 0.381

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