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- PDB-3u0c: Crystal structure of N-terminal region of Type III Secretion Firs... -

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Basic information

Entry
Database: PDB / ID: 3u0c
TitleCrystal structure of N-terminal region of Type III Secretion First Translocator IpaB (residues 74-224)
ComponentsInvasin ipaB
KeywordsCELL INVASION / translocator / type three secretion system / coiled-coil / virulence
Function / homology
Function and homology information


host cell membrane / host cell nucleus / 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
Type 3 secretion system translocon protein SctE
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsBarta, M.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 28, 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 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Invasin ipaB
B: Invasin ipaB


Theoretical massNumber of molelcules
Total (without water)44,9172
Polymers44,9172
Non-polymers00
Water1,58588
1
A: Invasin ipaB


Theoretical massNumber of molelcules
Total (without water)22,4581
Polymers22,4581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Invasin ipaB


Theoretical massNumber of molelcules
Total (without water)22,4581
Polymers22,4581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.419, 28.379, 104.806
Angle α, β, γ (deg.)90.00, 95.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Invasin ipaB / 62 kDa antigen


Mass: 22458.432 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 28-226)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaB, CP0128 / Plasmid: pT7HMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18011
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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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: 1.73 Å3/Da / Density % sol: 28.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.6 M sodium formate, 21% 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: 1.0000,1.0719
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 24, 2010 / Details: mirror
RadiationMonochromator: Si(220) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.07191
ReflectionResolution: 2.05→50 Å / Num. all: 19832 / Num. obs: 18186 / % possible obs: 91.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 13.4
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2.01 / % possible all: 59.3

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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: 2.05→26.066 Å / Occupancy max: 1 / Occupancy min: 0.79 / SU ML: 0.31 / σ(F): 0.06 / Phase error: 31.71 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2945 821 5 %
Rwork0.2454 --
obs0.2478 16416 82.76 %
all-19835 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.811 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.9165 Å20 Å29.5273 Å2
2--12.986 Å2-0 Å2
3----11.0695 Å2
Refinement stepCycle: LAST / Resolution: 2.05→26.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 0 88 2514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082440
X-RAY DIFFRACTIONf_angle_d1.0663266
X-RAY DIFFRACTIONf_dihedral_angle_d16.965986
X-RAY DIFFRACTIONf_chiral_restr0.057392
X-RAY DIFFRACTIONf_plane_restr0.006414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.17890.3761880.31861664X-RAY DIFFRACTION54
2.1789-2.3470.3341200.2952277X-RAY DIFFRACTION74
2.347-2.5830.39651400.29632672X-RAY DIFFRACTION85
2.583-2.95640.29521450.28312747X-RAY DIFFRACTION89
2.9564-3.7230.31831600.23793048X-RAY DIFFRACTION96
3.723-26.06850.24151680.20913187X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0452-0.08930.01110.10440.01320.0876-0.0969-0.0147-0.4994-0.1199-0.251-0.25280.12850.156900.41950.02570.05710.34270.00260.430112.1254-5.07748.9002
2-0.47480.0430.26150.63460.17720.88790.043-0.1817-0.08760.1459-0.17840.1086-0.03620.053500.3302-0.0463-0.02450.4176-0.02620.3876-16.24852.951559.2084
30.08970.18930.00390.0919-0.01780.09580.2710.0339-0.2377-0.1558-0.29450.2796-0.11-0.5495-00.32750.038-0.04050.296-0.02510.4314-16.94462.252841.445
40.08450.37980.16070.2833-0.46960.5527-0.4350.4985-0.29490.0506-0.02480.05950.7891-0.498200.4387-0.0318-0.03760.46640.00160.408110.8477-4.8992-2.7607
50.2204-0.24870.39870.3353-0.67390.4347-0.09370.0437-0.1629-0.0093-0.03910.0967-0.2867-0.1989-00.4059-0.0338-0.0320.3861-0.02060.376515.3051-3.717-16.1556
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 74:92)A74 - 92
2X-RAY DIFFRACTION2chain 'A' and (resseq 93:224)A93 - 224
3X-RAY DIFFRACTION3chain 'B' and (resseq 74:92)B74 - 92
4X-RAY DIFFRACTION4chain 'B' and (resseq 93:174)B93 - 174
5X-RAY DIFFRACTION5chain 'B' and (resseq 175:224)B175 - 224

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