[English] 日本語
Yorodumi
- PDB-4aky: CRYSTAL STRUCTURE OF VIRB8 FROM BRUCELLA SUIS IN COMPLEX WITH INT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4aky
TitleCRYSTAL STRUCTURE OF VIRB8 FROM BRUCELLA SUIS IN COMPLEX WITH INTERACTION INHIBITOR 2-(butylamino)-8-quinolinol
ComponentsTYPE IV SECRETION SYSTEM PROTEIN VIRB8
KeywordsTRANSPORT PROTEIN / BACTERIAL TYPE IV SECRETION
Function / homology
Function and homology information


protein secretion by the type IV secretion system / identical protein binding / plasma membrane
Similarity search - Function
VirB8 protein / Type IV secretion system protein VirB8/PtlE / Bacterial virulence protein VirB8 / VirB8 protein / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
2-(butylamino)quinolin-8-ol / Type IV secretion system protein virB8
Similarity search - Component
Biological speciesBRUCELLA SUIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCoincon, M. / Smith, M.A. / Sygusch, J. / Baron, C.
CitationJournal: Chem.Biol. / Year: 2012
Title: Identification of the Binding Site of Brucella Virb8 Interaction Inhibitors.
Authors: Smith, M.A. / Coincon, M. / Paschos, A. / Jolicoeur, B. / Lavallee, P. / Sygusch, J. / Baron, C.
History
DepositionFeb 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: TYPE IV SECRETION SYSTEM PROTEIN VIRB8
B: TYPE IV SECRETION SYSTEM PROTEIN VIRB8
C: TYPE IV SECRETION SYSTEM PROTEIN VIRB8
D: TYPE IV SECRETION SYSTEM PROTEIN VIRB8
E: TYPE IV SECRETION SYSTEM PROTEIN VIRB8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,76210
Polymers77,6815
Non-polymers1,0815
Water8,647480
1
A: TYPE IV SECRETION SYSTEM PROTEIN VIRB8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7522
Polymers15,5361
Non-polymers2161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TYPE IV SECRETION SYSTEM PROTEIN VIRB8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7522
Polymers15,5361
Non-polymers2161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TYPE IV SECRETION SYSTEM PROTEIN VIRB8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7522
Polymers15,5361
Non-polymers2161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TYPE IV SECRETION SYSTEM PROTEIN VIRB8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7522
Polymers15,5361
Non-polymers2161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: TYPE IV SECRETION SYSTEM PROTEIN VIRB8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7522
Polymers15,5361
Non-polymers2161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)198.440, 198.440, 103.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11B-2005-

HOH

21B-2014-

HOH

31B-2042-

HOH

41B-2081-

HOH

-
Components

#1: Protein
TYPE IV SECRETION SYSTEM PROTEIN VIRB8 / VIRB8


Mass: 15536.107 Da / Num. of mol.: 5 / Fragment: 97-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BRUCELLA SUIS (bacteria) / Plasmid: PET24D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q7CEG3
#2: Chemical
ChemComp-4LL / 2-(butylamino)quinolin-8-ol


Mass: 216.279 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C13H16N2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 3.27 Å3/Da / Density % sol: 62.39 % / Description: NONE
Crystal growpH: 7.6 / Details: 0.8 M K2HPO4, 0.04 M NA2HPO4 AND 1% DMSO, pH 7.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.6→48.6 Å / Num. obs: 31872 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 14.6 % / Biso Wilson estimate: 53.87 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 24.2
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 14.8 % / Mean I/σ(I) obs: 2 / Rsym value: 1.22 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BHM

2bhm


Resolution: 2.6→48.565 Å / SU ML: 0.44 / σ(F): 1.41 / Phase error: 23.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2364 2717 4.5 %
Rwork0.1976 --
obs0.1993 31867 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 90.602 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 55.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.9456 Å20 Å20 Å2
2--4.9456 Å20 Å2
3----9.8911 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5329 0 80 480 5889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095534
X-RAY DIFFRACTIONf_angle_d0.7337514
X-RAY DIFFRACTIONf_dihedral_angle_d13.2721929
X-RAY DIFFRACTIONf_chiral_restr0.047815
X-RAY DIFFRACTIONf_plane_restr0.003945
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.64740.31441430.26343071X-RAY DIFFRACTION100
2.6474-2.69830.34231400.25743019X-RAY DIFFRACTION100
2.6983-2.75330.27361410.24593056X-RAY DIFFRACTION100
2.7533-2.81320.30591410.22853045X-RAY DIFFRACTION100
2.8132-2.87860.3031430.23793062X-RAY DIFFRACTION100
2.8786-2.95060.3391460.22293021X-RAY DIFFRACTION100
2.9506-3.03040.2581450.21663074X-RAY DIFFRACTION100
3.0304-3.11950.25481390.19613054X-RAY DIFFRACTION100
3.1195-3.22020.2551420.17753013X-RAY DIFFRACTION100
3.2202-3.33530.18531460.16433043X-RAY DIFFRACTION100
3.3353-3.46880.18011400.16263037X-RAY DIFFRACTION100
3.4688-3.62660.22031450.1573056X-RAY DIFFRACTION100
3.6266-3.81770.24371420.15913057X-RAY DIFFRACTION100
3.8177-4.05680.19771410.16063027X-RAY DIFFRACTION100
4.0568-4.36990.15981430.13883055X-RAY DIFFRACTION100
4.3699-4.80930.17081490.1343018X-RAY DIFFRACTION100
4.8093-5.50430.20841440.17573068X-RAY DIFFRACTION100
5.5043-6.93170.25971410.24063041X-RAY DIFFRACTION100
6.9317-48.57340.28181460.25743055X-RAY DIFFRACTION100

+
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