[English] 日本語
Yorodumi
- PDB-1jx6: CRYSTAL STRUCTURE OF LUXP FROM VIBRIO HARVEYI COMPLEXED WITH AUTO... -

+
Open data


ID or keywords:

Loading...

-
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


outer membrane-bounded periplasmic space / carbohydrate binding
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more