[English] 日本語
Yorodumi
- PDB-2ixr: BipD of Burkholderia Pseudomallei -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ixr
TitleBipD of Burkholderia Pseudomallei
ComponentsMEMBRANE ANTIGEN
KeywordsTOXIN / BURKHOLDERIA PSEUDOMALLEI / BIPD / TTSS / T3SS / TYPE 3 SECRETION SYSTEM
Function / homologyIpaD-like / IpaD-like / Type III secretion systems tip complex components / BipD-like superfamily / Type III secretion systems tip complex components / Up-down Bundle / extracellular region / Mainly Alpha / Translocator protein BipD
Function and homology information
Biological speciesBURKHOLDERIA PSEUDOMALLEI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.6 Å
AuthorsRoversi, P. / Johnson, S. / Field, T. / Deane, J.E. / Galyov, E.E. / Lea, S.M.
Citation
Journal: J Biol Chem / Year: 2007
Title: Self-chaperoning of the type III secretion system needle tip proteins IpaD and BipD.
Authors: Steven Johnson / Pietro Roversi / Marianela Espina / Andrew Olive / Janet E Deane / Susan Birket / Terry Field / William D Picking / Ariel J Blocker / Edouard E Galyov / Wendy L Picking / Susan M Lea /
Abstract: Bacteria expressing type III secretion systems (T3SS) have been responsible for the deaths of millions worldwide, acting as key virulence elements in diseases ranging from plague to typhoid fever. ...Bacteria expressing type III secretion systems (T3SS) have been responsible for the deaths of millions worldwide, acting as key virulence elements in diseases ranging from plague to typhoid fever. The T3SS is composed of a basal body, which traverses both bacterial membranes, and an external needle through which effector proteins are secreted. We report multiple crystal structures of two proteins that sit at the tip of the needle and are essential for virulence: IpaD from Shigella flexneri and BipD from Burkholderia pseudomallei. The structures reveal that the N-terminal domains of the molecules are intramolecular chaperones that prevent premature oligomerization, as well as sharing structural homology with proteins involved in eukaryotic actin rearrangement. Crystal packing has allowed us to construct a model for the tip complex that is supported by mutations designed using the structure.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Expression, Purification, Crystallization and Preliminary Crystallographic Analysis of Bipd, a Component of the Burkholderia Pseudomallei Type III Secretion System.
Authors: Roversi, P. / Johnson, S. / Field, T. / Deane, J.E. / Galyov, E.E. / Lea, S.M.
History
DepositionJul 10, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MEMBRANE ANTIGEN


Theoretical massNumber of molelcules
Total (without water)33,0871
Polymers33,0871
Non-polymers00
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)103.980, 122.790, 49.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

-
Components

#1: Protein MEMBRANE ANTIGEN / BIPD


Mass: 33087.219 Da / Num. of mol.: 1 / Fragment: RESIDUES 10-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA PSEUDOMALLEI (bacteria) / Strain: 10276
Description: PUBLIC HEALTH LABORATORY SERVICE, COLINDALE, LONDON, UK
Plasmid: PGEXBIPD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q63K37
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE GS INITIAL RESIDUES COME FROM THE TAG, THE SEQUENCE STARTS AT BIPD RESIDUE 10

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 47 %
Description: TWO PT ATOMS WERE FOUND IN K2PTCL4 ANOMALOUS DIFFERENCE PATTERSON MAPS USING SHELXD. THESE PT SITES ALLOWED LOCATION OF THE SE ATOMS IN A SEMET DERIVATIVE ANOMALOUS FOURIER DIFFERENCE MAP USING SHARP.
Crystal growpH: 8.5 / Details: 1 M TRISODIUM CITRATE, 10 MM SODIUM BORATE PH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9778
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 23, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.6→38.1 Å / Num. obs: 10013 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 3.1 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.7
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 5.4 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
DMmodel building
SCALAdata scaling
SHELXDphasing
SHARPphasing
SOLOMONphasing
DMphasing
TNT5.6.1refinement
RefinementMethod to determine structure: MIRAS / Resolution: 2.6→40 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: TNT WAS DRIVEN BY MAXIMUM LIKELIHOOD USING BUSTER BETA 1.0.3
RfactorNum. reflection
Rwork0.2 -
all0.205 10013
obs0.2 10013
Solvent computationSolvent model: BABINET SCALING / Bsol: 51 Å2 / ksol: 0.39 e/Å3
Refinement stepCycle: LAST / Resolution: 2.6→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1993 0 0 50 2043
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00520512
X-RAY DIFFRACTIONt_angle_deg0.41627655
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.006662
X-RAY DIFFRACTIONt_gen_planes0.0112915
X-RAY DIFFRACTIONt_it0.982205120
X-RAY DIFFRACTIONt_nbd0.034375
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact

+
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