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- PDB-2hj9: Crystal structure of the Autoinducer-2-bound form of Vibrio harve... -

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Basic information

Entry
Database: PDB / ID: 2hj9
TitleCrystal structure of the Autoinducer-2-bound form of Vibrio harveyi LuxP complexed with the periplasmic domain of LuxQ
Components
  • Autoinducer 2 sensor kinase/phosphatase luxQ
  • Autoinducer 2-binding periplasmic protein luxP
KeywordsSIGNALING PROTEIN / PERIPLASMIC BINDING PROTEIN / PER/ARNT/SIMPLE-MINDED (PAS) FOLD / AUTOINDUCER-2 (AI-2) / QUORUM SENSING / HISTIDINE SENSOR KINASE
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 / outer membrane-bounded periplasmic space / carbohydrate binding / 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 / Periplasmic binding protein / Periplasmic binding protein domain / His Kinase A (phospho-acceptor) 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 / Periplasmic binding protein / Periplasmic binding protein domain / 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 / Response regulator / Single Sheet / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Periplasmic binding protein-like I / Histidine kinase/HSP90-like ATPase superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-AI2 / Autoinducer 2-binding periplasmic protein LuxP / Autoinducer 2 sensor kinase/phosphatase LuxQ
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsNeiditch, M.B. / Hughson, F.M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Ligand-induced asymmetry in histidine sensor kinase complex regulates quorum sensing.
Authors: Neiditch, M.B. / Federle, M.J. / Pompeani, A.J. / Kelly, R.C. / Swem, D.L. / Jeffrey, P.D. / Bassler, B.L. / Hughson, F.M.
History
DepositionJun 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE TWO HETEROLOGOUS LUXQ N-TERMINAL RESIDUES (GLY-SER) ARE DERIVED FROM THE THROMBIN ...SEQUENCE THE TWO HETEROLOGOUS LUXQ N-TERMINAL RESIDUES (GLY-SER) ARE DERIVED FROM THE THROMBIN CLEAVAGE SIGNAL. LUXP RESIDUES 22-26 ARE DELETED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Autoinducer 2-binding periplasmic protein luxP
B: Autoinducer 2-binding periplasmic protein luxP
C: Autoinducer 2 sensor kinase/phosphatase luxQ
D: Autoinducer 2 sensor kinase/phosphatase luxQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,6026
Polymers127,2164
Non-polymers3862
Water7,098394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.916, 83.916, 365.328
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Autoinducer 2-binding periplasmic protein luxP


Mass: 38739.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Gene: luxP / Plasmid: PGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P54300
#2: Protein Autoinducer 2 sensor kinase/phosphatase luxQ


Mass: 24868.869 Da / Num. of mol.: 2 / Fragment: periplasmic domain (residues 53-271)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Gene: luxQ / Plasmid: PGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P54302, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#3: Chemical ChemComp-AI2 / 3A-METHYL-5,6-DIHYDRO-FURO[2,3-D][1,3,2]DIOXABOROLE-2,2,6,6A-TETRAOL / (2S,3R,4S)-2-METHYL-3,4-DIHYDROXY-OXOLAN-2,3-DIOXY-BORATE


Mass: 192.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10BO7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 1:1 mixture of protein (20 mg/ml in 20 mM Tris-HCl (pH 7.5), 150 mM NaCl) and well solution (27.5% (w/v) PEG 400, 100 mM potassium nitrate, 100 mM 2-morpholinoethanesulfonic acid monohydrate ...Details: 1:1 mixture of protein (20 mg/ml in 20 mM Tris-HCl (pH 7.5), 150 mM NaCl) and well solution (27.5% (w/v) PEG 400, 100 mM potassium nitrate, 100 mM 2-morpholinoethanesulfonic acid monohydrate (pH 6.0), 100 M 4,5-dihydroxy-2,3-pentane dione, and 1 mM boric acid), VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2005
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.34→30 Å / Num. obs: 55573 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.34→2.42 Å / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→29.7 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.266 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.369 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26178 2827 5.1 %RANDOM
Rwork0.20689 ---
obs0.20966 52723 98.39 %-
all-52728 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.523 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20 Å2
2--0.76 Å20 Å2
3----1.51 Å2
Refinement stepCycle: LAST / Resolution: 2.34→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8674 0 26 394 9094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228900
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.94712106
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23851074
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.1924.501451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.414151463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8581549
X-RAY DIFFRACTIONr_chiral_restr0.1150.21350
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026837
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.24218
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.26094
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2559
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7261.55514
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.30228747
X-RAY DIFFRACTIONr_scbond_it1.76433817
X-RAY DIFFRACTIONr_scangle_it2.7754.53359
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.34→2.4 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 192 -
Rwork0.259 3720 -
obs--96.19 %

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