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- PDB-2j9t: BipD of Burkholderia Pseudomallei -

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Basic information

Entry
Database: PDB / ID: 2j9t
TitleBipD of Burkholderia Pseudomallei
ComponentsMEMBRANE ANTIGEN
KeywordsTOXIN / BURKHOLDERIA PSEUDOMALLEI / BIPD / TTSS / T3SS / TYPE 3 SECRETION SYSTEM
Function / homology
Function and homology information


extracellular region
Similarity search - Function
IpaD-like / IpaD-like / Type III secretion systems tip complex components / BipD-like superfamily / Type III secretion systems tip complex components / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BORIC ACID / CITRATE ANION / Translocator protein BipD
Similarity search - Component
Biological speciesBURKHOLDERIA PSEUDOMALLEI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.7 Å
AuthorsJohnson, 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
DepositionNov 16, 2006Deposition site: PDBE / Processing site: PDBE
SupersessionNov 20, 2006ID: 2CMQ
Revision 1.0Nov 20, 2006Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MEMBRANE ANTIGEN
B: MEMBRANE ANTIGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4875
Polymers66,1742
Non-polymers3133
Water79344
1
A: MEMBRANE ANTIGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3383
Polymers33,0871
Non-polymers2512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: MEMBRANE ANTIGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1492
Polymers33,0871
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)136.470, 89.840, 50.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.57394, -0.81879, 0.0131), (-0.81888, 0.57395, -0.00339), (-0.00475, -0.01267, -0.99991)
Vector: 180.89531, 94.27765, 14.58168)

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Components

#1: Protein MEMBRANE ANTIGEN / BIPD


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 ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BH3O3
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.8 % / Description: PHASED WITH K2PTCL4 AND SEMET DERIVATIVES
Crystal growpH: 8.5 / Details: 1 M TRISODIUM CITRATE, 10 MM SODIUM BORATE PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.7→2.85 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
TNT5.6.1refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
SHARPphasing
SOLOMONphasing
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.26 887 0.1 %0.213
Rwork0.21 ---
all0.213 ---
obs0.21 17569 --
Solvent computationSolvent model: BABINET SCALING / Bsol: 55 Å2 / ksol: 0.388 e/Å3
Refinement stepCycle: LAST / Resolution: 2.7→54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3928 0 21 44 3993
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00439981
X-RAY DIFFRACTIONt_angle_deg0.53153871
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0041292
X-RAY DIFFRACTIONt_gen_planes0.0095765
X-RAY DIFFRACTIONt_it0.926399820
X-RAY DIFFRACTIONt_nbd0.029705
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

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