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- PDB-1jx6: CRYSTAL STRUCTURE OF LUXP FROM VIBRIO HARVEYI COMPLEXED WITH AUTO... -

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Basic information

Entry
Database: PDB / ID: 1jx6
TitleCRYSTAL STRUCTURE OF LUXP FROM VIBRIO HARVEYI COMPLEXED WITH AUTOINDUCER-2
ComponentsLUXP PROTEIN
KeywordsSIGNALING PROTEIN / PROTEIN-LIGAND COMPLEX
Function / homology
Function and homology information


periplasmic space / transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AI2 / Autoinducer 2-binding periplasmic protein LuxP
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.5 Å
AuthorsChen, X. / Schauder, S. / Potier, N. / Van Dorsselaer, A. / Pelczer, I. / BassleR, B.L. / Hughson, F.M.
CitationJournal: Nature / Year: 2002
Title: Structural identification of a bacterial quorum-sensing signal containing boron.
Authors: Chen, X. / Schauder, S. / Potier, N. / Van Dorsselaer, A. / Pelczer, I. / Bassler, B.L. / Hughson, F.M.
History
DepositionSep 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

Downloads & links

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Assembly

Deposited unit
A: LUXP PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2993
Polymers39,0661
Non-polymers2332
Water5,981332
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.268, 77.467, 52.008
Angle α, β, γ (deg.)90.00, 96.37, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsPROBABLY MONOMER

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Components

#1: Protein LUXP PROTEIN


Mass: 39065.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Gene: LUXP / Plasmid: PGEX4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P54300
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#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.: 1 / Source method: obtained synthetically / Formula: C5H10BO7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, GLYCEROL, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlLuxP11
20.1 MTris-HCl11pH8.5
315 %PEG400011
418 %(v/v)glycerol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.072 Å
DetectorType: BRANDEIS / Detector: CCD / Date: Apr 14, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.45→25 Å / Num. all: 61620 / Num. obs: 61620 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.036 / Net I/σ(I): 42
Reflection shellResolution: 1.45→1.5 Å / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 3.6 / Num. unique all: 6131 / Rsym value: 0.297 / % possible all: 100
Reflection
*PLUS
% possible obs: 100 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.035
Reflection shell
*PLUS
Rmerge(I) obs: 0.25

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
MARMADdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.5→24.58 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 542802.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 4196 8.1 %RANDOM
Rwork0.214 ---
all0.216 55782 --
obs0.214 51487 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.4898 Å2 / ksol: 0.358532 e/Å3
Displacement parametersBiso mean: 25.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.56 Å20 Å20.73 Å2
2---2.23 Å20 Å2
3---5.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-25 Å
Luzzati sigma a0.19 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.5→24.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 14 332 3073
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it3.085
X-RAY DIFFRACTIONc_mcangle_it3.617
X-RAY DIFFRACTIONc_scbond_it4.496
X-RAY DIFFRACTIONc_scangle_it5.918
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.317 359 8.3 %
Rwork0.274 3945 -
obs-3945 77.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3AI2.PARAMAI2.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / Num. reflection obs: 53816 / σ(F): 1 / % reflection Rfree: 8.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75
X-RAY DIFFRACTIONc_mcbond_it3.085
X-RAY DIFFRACTIONc_scbond_it4.496
X-RAY DIFFRACTIONc_mcangle_it3.617
X-RAY DIFFRACTIONc_scangle_it5.918
LS refinement shell
*PLUS
Rfactor Rfree: 0.317 / % reflection Rfree: 8.3 % / Rfactor Rwork: 0.274 / Rfactor obs: 0.274

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