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- PDB-2izp: BipD - an invasion protein associated with the type-III secretion... -

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Basic information

Entry
Database: PDB / ID: 2izp
TitleBipD - an invasion protein associated with the type-III secretion system of Burkholderia pseudomallei.
ComponentsPUTATIVE MEMBRANE ANTIGEN
KeywordsTOXIN / VIRULENCE FACTOR / INVASION PROTEIN / TYPE-III 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 / MAD / Resolution: 2.1 Å
AuthorsErskine, P.T. / Knight, M.J. / Ruaux, A. / Mikolajek, H. / Wong-Fat-Sang, N. / Withers, J. / Gill, R. / Wood, S.P. / Wood, M. / Fox, G.C. / Cooper, J.B.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: High Resolution Structure of Bipd: An Invasion Protein Associated with the Type III Secretion System of Burkholderia Pseudomallei.
Authors: Erskine, P.T. / Knight, M.J. / Ruaux, A. / Mikolajek, H. / Wong-Fat-Sang, N. / Withers, J. / Gill, R. / Wood, S.P. / Wood, M. / Fox, G.C. / Cooper, J.B.
History
DepositionJul 25, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 14, 2019Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.4May 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUTATIVE MEMBRANE ANTIGEN
B: PUTATIVE MEMBRANE ANTIGEN


Theoretical massNumber of molelcules
Total (without water)66,1742
Polymers66,1742
Non-polymers00
Water12,268681
1
A: PUTATIVE MEMBRANE ANTIGEN


Theoretical massNumber of molelcules
Total (without water)33,0871
Polymers33,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PUTATIVE MEMBRANE ANTIGEN


Theoretical massNumber of molelcules
Total (without water)33,0871
Polymers33,0871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.509, 56.204, 84.208
Angle α, β, γ (deg.)90.00, 94.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PUTATIVE MEMBRANE ANTIGEN / BIPD


Mass: 33087.219 Da / Num. of mol.: 2 / Fragment: RESIDUES 8-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA PSEUDOMALLEI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q63K37
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 681 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CLONING STRATEGY MEANS THAT THE EXPRESSED PROTEIN STARTS AT RESIDUE GLY 8 AND THE FOLLOWING ...THE CLONING STRATEGY MEANS THAT THE EXPRESSED PROTEIN STARTS AT RESIDUE GLY 8 AND THE FOLLOWING RESIDUE IS SER INSTEAD OF ARG IN THE CORRECT SEQUENCE. NONE OF THESE RESIDUES WERE VISIBLE IN THE ELECTRON DENSITY ANYHOW.

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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: 1.9 Å3/Da / Density % sol: 35 %
Crystal growpH: 5.8
Details: [BIPD]=4 MG/ML, 20-25% PEG 4000, 5MM NICKEL CHLORIDE, 0.1M GLYCINE, 0.1M SODIUM CACODYLATE PH 5.0-5.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.97935
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 104464 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.4
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.8 / % possible all: 93.4

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Processing

Software
NameClassification
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→10 Å / Num. parameters: 19327 / Num. restraintsaints: 17256 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1394 5 %THIN SHELLS
obs0.226 -97.5 %-
all-28267 --
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4164 0 0 681 4845
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d0.017
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.022
X-RAY DIFFRACTIONs_zero_chiral_vol0.022
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.024
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.014
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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