+Open data
-Basic information
Entry | Database: PDB / ID: 2j9t | |||||||||
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Title | BipD of Burkholderia Pseudomallei | |||||||||
Components | MEMBRANE ANTIGEN | |||||||||
Keywords | TOXIN / BURKHOLDERIA PSEUDOMALLEI / BIPD / TTSS / T3SS / TYPE 3 SECRETION SYSTEM | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | BURKHOLDERIA PSEUDOMALLEI (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.7 Å | |||||||||
Authors | Johnson, S. / Roversi, P. / Field, T. / Deane, J.E. / Galyov, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j9t.cif.gz | 109.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j9t.ent.gz | 85.3 KB | Display | PDB format |
PDBx/mmJSON format | 2j9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j9t_validation.pdf.gz | 474.8 KB | Display | wwPDB validaton report |
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Full document | 2j9t_full_validation.pdf.gz | 495 KB | Display | |
Data in XML | 2j9t_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 2j9t_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/2j9t ftp://data.pdbj.org/pub/pdb/validation_reports/j9/2j9t | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.57394, -0.81879, 0.0131), Vector: |
-Components
#1: Protein | Mass: 33087.219 Da / Num. of mol.: 2 / 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: Chemical | #3: Chemical | ChemComp-FLC / | #4: Water | ChemComp-HOH / | Sequence details | THE GS INITIAL RESIDUES COME FROM THE TAG, THE SEQUENCE STARTS AT BIPD RESIDUE 10 | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.8 % / Description: PHASED WITH K2PTCL4 AND SEMET DERIVATIVES |
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Crystal grow | pH: 8.5 / Details: 1 M TRISODIUM CITRATE, 10 MM SODIUM BORATE PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 9, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→54.31 Å / Num. obs: 114952 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 3.6 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.7→54 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO Details: TNT RUN AGAINST MAXIMUM LIKELIHOOD IN BUSTER-TNT 1.9.3. BORIC ACID FROM BUFFER
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Solvent computation | Solvent model: BABINET SCALING / Bsol: 55 Å2 / ksol: 0.388 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→54 Å
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Refine LS restraints |
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