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- PDB-2fqt: Crystal structure of B.subtilis LuxS in complex with (2S)-2-Amino... -

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Basic information

Entry
Database: PDB / ID: 2fqt
TitleCrystal structure of B.subtilis LuxS in complex with (2S)-2-Amino-4-[(2R,3S)-2,3-dihydroxy-3-N-hydroxycarbamoyl-propylmercapto]butyric acid
ComponentsS-ribosylhomocysteine lyase
KeywordsLYASE / LuxS / Quorum sensing
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
: / Chem-H1D / S-ribosylhomocysteine lyase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.79 Å
AuthorsShen, G. / Rajan, R. / Zhu, J. / Bell, C.E. / Pei, D.
CitationJournal: J.Med.Chem. / Year: 2006
Title: Design and Synthesis of Substrate Analogue Inhibitors of S-Ribosylhomocysteinase (LuxS)
Authors: Shen, G. / Rajan, R. / Zhu, J. / Bell, C.E. / Pei, D.
History
DepositionJan 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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

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Assembly

Deposited unit
A: S-ribosylhomocysteine lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2585
Polymers17,7381
Non-polymers5194
Water2,468137
1
A: S-ribosylhomocysteine lyase
hetero molecules

A: S-ribosylhomocysteine lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,51510
Polymers35,4762
Non-polymers1,0398
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area5040 Å2
ΔGint-82 kcal/mol
Surface area12580 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.860, 62.860, 148.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-528-

HOH

DetailsThe active dimer is formed by the application of the symmetry operator X,X-Y,-Z+5/6 to the contents of the asymetric unit.

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Components

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


Mass: 17738.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: luxS / Plasmid: pET22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O34667, S-ribosylhomocysteine lyase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-H1D / (2S)-2-AMINO-4-[(2R,3S)-2,3-DIHYDROXY-3-N-HYDROXYCARBAMOYL-PROPYLMERCAPTO]BUTYRIC ACID


Mass: 268.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16N2O6S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 2.2M Ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2005 / Details: osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.79→20.38 Å / Num. all: 15622 / Num. obs: 15622 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.194 / Net I/σ(I): 17.2
Reflection shellResolution: 1.79→1.86 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 3.9 / Num. unique all: 1004 / % possible all: 54.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClearD*TREK (MSC/RIGAKU)data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1YCL

1ycl


Resolution: 1.79→20.38 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 594455.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1568 10 %RANDOM
Rwork0.194 ---
obs0.194 15622 91.1 %-
all-15622 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.5067 Å2 / ksol: 0.412927 e/Å3
Displacement parametersBiso mean: 21.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å2-1.03 Å20 Å2
2--1.04 Å20 Å2
3----2.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.79→20.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1221 0 28 137 1386
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.532
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it2.942.5
LS refinement shellResolution: 1.79→1.9 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 158 9.6 %
Rwork0.268 1491 -
obs--59.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3276ref.param276ref.top
X-RAY DIFFRACTION5ion.paramion.top

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