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- PDB-3tul: Crystal structure of N-terminal region of Type III Secretion Majo... -

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Basic information

Entry
Database: PDB / ID: 3tul
TitleCrystal structure of N-terminal region of Type III Secretion Major Translocator SipB (residues 82-226)
ComponentsCell invasion protein sipB
KeywordsCELL INVASION / translocator / type three secretion system / coiled-coil / virulence
Function / homology
Function and homology information


protein localization to Golgi apparatus / host cell membrane / killing of cells of another organism / extracellular region / membrane
Similarity search - Function
Type III secretion system, invasin protein B / Invasin IpaB, N-terminal / Type III cell invasion protein SipB / Secretion system effector C, SseC-like / Secretion system effector C (SseC) like family / Nucleotidyltransferases domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
SPI-1 type 3 secretion system translocon protein SctE
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.793 Å
AuthorsBarta, M.L. / Dickenson, N.E. / Patel, M. / Keightley, J.A. / Picking, W.D. / Picking, W.L. / Geisbrecht, B.V.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: The Structures of Coiled-Coil Domains from Type III Secretion System Translocators Reveal Homology to Pore-Forming Toxins.
Authors: Barta, M.L. / Dickenson, N.E. / Patil, M. / Keightley, A. / Wyckoff, G.J. / Picking, W.D. / Picking, W.L. / Geisbrecht, B.V.
History
DepositionSep 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell invasion protein sipB
B: Cell invasion protein sipB
C: Cell invasion protein sipB
D: Cell invasion protein sipB


Theoretical massNumber of molelcules
Total (without water)67,3534
Polymers67,3534
Non-polymers00
Water77543
1
A: Cell invasion protein sipB


Theoretical massNumber of molelcules
Total (without water)16,8381
Polymers16,8381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell invasion protein sipB


Theoretical massNumber of molelcules
Total (without water)16,8381
Polymers16,8381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cell invasion protein sipB


Theoretical massNumber of molelcules
Total (without water)16,8381
Polymers16,8381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cell invasion protein sipB


Theoretical massNumber of molelcules
Total (without water)16,8381
Polymers16,8381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-56 kcal/mol
Surface area30230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.154, 51.144, 84.646
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein
Cell invasion protein sipB / Effector protein sipB


Mass: 16838.328 Da / Num. of mol.: 4 / Fragment: N-terminal domain (UNP residues 81-237)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: sipB, sspB, STM2885 / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q56019
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.15 M potassium bromide, 27% PEG2000 MME, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97243,0.97934
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 16, 2011 / Details: mirror
RadiationMonochromator: Si(220) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.972431
20.979341
ReflectionResolution: 2.793→31.943 Å / Num. all: 17834 / Num. obs: 17478 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 12 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.8
Reflection shellResolution: 2.793→2.9681 Å / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 2.55 / % possible all: 80

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.793→31.943 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 0.26 / Phase error: 34.67 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3164 841 5 %
Rwork0.298 --
obs0.299 16819 94.32 %
all-17854 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.993 Å2 / ksol: 0.266 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.2106 Å2-0 Å20 Å2
2--10.9258 Å20 Å2
3----5.7152 Å2
Refinement stepCycle: LAST / Resolution: 2.793→31.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3876 0 0 43 3919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093884
X-RAY DIFFRACTIONf_angle_d1.245206
X-RAY DIFFRACTIONf_dihedral_angle_d17.3811452
X-RAY DIFFRACTIONf_chiral_restr0.077637
X-RAY DIFFRACTIONf_plane_restr0.003661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.793-2.96810.39171160.38582196X-RAY DIFFRACTION80
2.9681-3.1970.35761360.34332602X-RAY DIFFRACTION93
3.197-3.51840.34431430.33272712X-RAY DIFFRACTION98
3.5184-4.02670.31291440.27812747X-RAY DIFFRACTION98
4.0267-5.06990.28961470.26312799X-RAY DIFFRACTION99
5.0699-31.9450.29371550.28662922X-RAY DIFFRACTION98

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