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- PDB-3c30: Crystal structure of the Vibrio Cholerae LuxQ periplasmic domain ... -

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Basic information

Entry
Database: PDB / ID: 3c30
TitleCrystal structure of the Vibrio Cholerae LuxQ periplasmic domain (SeMet)
ComponentsAutoinducer 2 sensor kinase/phosphatase luxQ
Keywordssignaling protein / transferase / 2-Component System / Quorum Sensing / Histidine Kinase / Hydrolase / Inner membrane / Membrane / Phosphoprotein / Protein phosphatase / Transmembrane / Two-component regulatory system
Function / homology
Function and homology information


histidine phosphotransfer kinase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / histidine kinase / phosphoprotein phosphatase activity / phosphorelay sensor kinase activity / ATP binding / plasma membrane
Similarity search - Function
LuxQ periplasmic domain, C-terminal subdomain / LuxQ periplasmic domain, N-terminal subdomain / LuxQ, periplasmic domain / LuxQ periplasmic domain, N-terminal subdomain / LuxQ, periplasmic / Anthopleurin-A / Periplasmic sensor-like domain superfamily / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain ...LuxQ periplasmic domain, C-terminal subdomain / LuxQ periplasmic domain, N-terminal subdomain / LuxQ, periplasmic domain / LuxQ periplasmic domain, N-terminal subdomain / LuxQ, periplasmic / Anthopleurin-A / Periplasmic sensor-like domain superfamily / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Beta-Lactamase / Single Sheet / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Autoinducer 2 sensor kinase/phosphatase LuxQ
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsSlama, B. / Hendrickson, W.
CitationJournal: To be Published
Title: Crystal structure of the Vibrio Cholerae LuxQ periplasmic domain (SeMet)
Authors: Slama, B. / Hendrickson, W.
History
DepositionJan 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Autoinducer 2 sensor kinase/phosphatase luxQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5202
Polymers30,3251
Non-polymers1951
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.584, 55.584, 160.959
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Autoinducer 2 sensor kinase/phosphatase luxQ


Mass: 30325.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: luxQ / Plasmid: pET15 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9KLK7, histidine kinase, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.05 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12% v/v PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 19, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.8→27.86 Å / Num. obs: 11874 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Redundancy: 12 % / Biso Wilson estimate: 104.9 Å2 / Rsym value: 6.7 / Net I/σ(I): 21.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementResolution: 2.8→27.86 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1424021 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.228 562 4.8 %RANDOM
Rwork0.201 ---
obs0.201 11826 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.4913 Å2 / ksol: 0.332045 e/Å3
Displacement parametersBiso mean: 45.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.8→27.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 12 92 1844
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.751.5
X-RAY DIFFRACTIONc_mcangle_it3.172
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it3.212.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.287 87 4.5 %
Rwork0.267 1842 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3mes+pegs_xplor_par.txt

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