[English] 日本語
Yorodumi
- PDB-4yr7: Structure of LuxP In Complex With 1-deoxy-alpha-L-xylulofuranose-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yr7
TitleStructure of LuxP In Complex With 1-deoxy-alpha-L-xylulofuranose-1,2-borate
ComponentsAutoinducer 2-binding periplasmic protein LuxP
KeywordsSIGNALING PROTEIN / PROTEIN-LIGAND COMPLEX / QUORUM SENSING
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
1-deoxy-alpha-L-xylulofuranose-1,2-borate / Autoinducer 2-binding periplasmic protein LuxP
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.533 Å
AuthorsMcDonough, M.A. / Sattin, S. / Davis, B.G.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/D023343/1, EP/D023327/1, EP/E000614/1 United Kingdom
Royal Society United Kingdom
CitationJournal: To Be Published
Title: Discovery of Glycomimetic Agonists from a Protocell Metabolism, Proto-natural Product Libraries
Authors: Sattin, S. / McDonough, M.A. / Davis, B.G.
History
DepositionMar 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 2.0Sep 13, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_validate_close_contact / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Autoinducer 2-binding periplasmic protein LuxP
B: Autoinducer 2-binding periplasmic protein LuxP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0364
Polymers78,6822
Non-polymers3542
Water3,513195
1
A: Autoinducer 2-binding periplasmic protein LuxP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5182
Polymers39,3411
Non-polymers1771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Autoinducer 2-binding periplasmic protein LuxP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5182
Polymers39,3411
Non-polymers1771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.450, 85.230, 133.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Autoinducer 2-binding periplasmic protein LuxP


Mass: 39341.055 Da / Num. of mol.: 2 / Fragment: UNP residues 21-365
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Gene: luxP / Plasmid: pGEX4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P54300
#2: Chemical ChemComp-A1B / 1-deoxy-alpha-L-xylulofuranose-1,2-borate


Mass: 176.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10BO6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 12% polyethylene glycol, 100 mM sodium cacodylate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.53→85.23 Å / Num. obs: 29003 / % possible obs: 100 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.068 / Rsym value: 0.026 / Net I/σ(I): 16.5
Reflection shellResolution: 2.53→2.6 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 2.7 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JX6

1jx6


Resolution: 2.533→71.854 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2025 1473 5.09 %
Rwork0.1507 --
obs0.1534 28925 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.533→71.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5420 0 24 195 5639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015603
X-RAY DIFFRACTIONf_angle_d1.267618
X-RAY DIFFRACTIONf_dihedral_angle_d16.0482048
X-RAY DIFFRACTIONf_chiral_restr0.078825
X-RAY DIFFRACTIONf_plane_restr0.005990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5335-2.61530.37551290.28732447X-RAY DIFFRACTION100
2.6153-2.70870.3131560.22372433X-RAY DIFFRACTION100
2.7087-2.81720.27421310.19752451X-RAY DIFFRACTION100
2.8172-2.94540.24481420.18472465X-RAY DIFFRACTION100
2.9454-3.10070.27651240.18852472X-RAY DIFFRACTION100
3.1007-3.2950.25861250.192475X-RAY DIFFRACTION100
3.295-3.54940.22711390.16462488X-RAY DIFFRACTION100
3.5494-3.90660.20251370.14062488X-RAY DIFFRACTION100
3.9066-4.47180.16041190.12252518X-RAY DIFFRACTION100
4.4718-5.63360.16281500.11732534X-RAY DIFFRACTION100
5.6336-71.88250.17631210.14522681X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.15330.18393.02252.22495.1897.82150.0112-0.41930.01580.36611.0093-1.47350.1931.8035-1.06370.5009-0.0474-0.06620.77020.07860.59419.9021-26.434724.8928
23.60961.3292-0.9395.4713-0.07425.9087-0.0530.1021-0.2994-0.07190.10350.21260.1865-0.075-0.02730.2837-0.0092-0.0450.3561-0.01990.3383-9.3741-35.451216.4758
34.5367-1.2104-1.80475.62381.31163.0646-0.0518-0.5944-0.240.88230.01790.039-0.00530.2979-0.00020.466-0.0327-0.03530.5110.08490.3487-8.7374-26.409830.8788
40.9-0.0726-0.06546.4103-0.98991.09670.04480.1808-0.073-0.2441-0.087-0.2723-0.06650.25450.05040.31540.00720.01560.51610.0090.3271-2.0314-12.997810.9167
52.5433-0.0238.44942.37282.84662.4390.6948-0.1973-0.61420.2444-0.022-0.08590.576-0.1751-1.10750.6820.02340.05780.61640.02630.6278-29.0996-72.15318.9874
66.7341-0.0729-1.08354.0631-0.06995.4438-0.13830.25660.8879-0.0405-0.1828-0.7745-0.15510.30640.31850.3965-0.0152-0.11410.41070.08960.6372-19.2212-52.952916.5226
74.4942-0.14311.57864.8919-2.18235.0993-0.14220.74790.6165-0.4138-0.1088-0.3129-0.17060.48370.24550.46450.0061-0.00290.52360.12270.493-28.4659-51.85773.1038
85.8035-0.4446-1.36130.3492-0.05321.6107-0.1734-0.16470.16910.13590.0484-0.14960.0755-0.04180.13090.450.0297-0.07870.2549-0.00350.3994-41.0119-59.485121.2692
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 112 )
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 173 )
4X-RAY DIFFRACTION4chain 'A' and (resid 174 through 364 )
5X-RAY DIFFRACTION5chain 'B' and (resid 26 through 53 )
6X-RAY DIFFRACTION6chain 'B' and (resid 54 through 112 )
7X-RAY DIFFRACTION7chain 'B' and (resid 113 through 164 )
8X-RAY DIFFRACTION8chain 'B' and (resid 165 through 365 )

+
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://pdbjlvh1.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