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- PDB-5wkq: 2.10 A resolution structure of IpaB (residues 74-242) from Shigel... -

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Basic information

Entry
Database: PDB / ID: 5wkq
Title2.10 A resolution structure of IpaB (residues 74-242) from Shigella flexneri
ComponentsInvasin IpaB
KeywordsMEMBRANE PROTEIN / Shigella / type III secretion / T3SS / IpaB / translocon
Function / homology
Function and homology information


host cell membrane / host cell / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBarta, M.L. / Lovell, S. / Battaile, K.P. / Picking, W.L. / Picking, W.D.
CitationJournal: Protein Sci. / Year: 2018
Title: Using disruptive insertional mutagenesis to identify the in situ structure-function landscape of the Shigella translocator protein IpaB.
Authors: Barta, M.L. / Tachiyama, S. / Muthuramalingam, M. / Arizmendi, O. / Villanueva, C.E. / Ramyar, K.X. / Geisbrecht, B.V. / Lovell, S. / Battaile, K.P. / Picking, W.L. / Picking, W.D.
History
DepositionJul 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Invasin IpaB
B: Invasin IpaB


Theoretical massNumber of molelcules
Total (without water)39,1562
Polymers39,1562
Non-polymers00
Water3,135174
1
A: Invasin IpaB


Theoretical massNumber of molelcules
Total (without water)19,5781
Polymers19,5781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Invasin IpaB


Theoretical massNumber of molelcules
Total (without water)19,5781
Polymers19,5781
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.429, 171.429, 40.591
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Invasin IpaB / 62 kDa antigen


Mass: 19578.061 Da / Num. of mol.: 2 / Fragment: UNP residues 74-242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaB, CP0128 / Production host: Escherichia coli (E. coli) / References: UniProt: P18011
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 3.88 Å3/Da / Density % sol: 68.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.2 M ammonium acetate, 0.1 M sodium acetate (pH 4.0) and 15% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→42.86 Å / Num. obs: 34988 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 38.5 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.1 / Num. measured all: 233850 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.1-2.166.60.9811881428620.8022100
8.91-42.866.30.0631565040.99728.196.4

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.5.32data scaling
PDB_EXTRACT3.22data extraction
Aimlessdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U0C

3u0c


Resolution: 2.1→35.873 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 27.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 1683 4.81 %Random selection
Rwork0.2005 33279 --
obs0.2027 34962 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.61 Å2 / Biso mean: 58.0747 Å2 / Biso min: 22.92 Å2
Refinement stepCycle: final / Resolution: 2.1→35.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2475 0 0 174 2649
Biso mean---48.61 -
Num. residues----323
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.16180.36331490.304227482897100
2.1618-2.23160.2681340.262727492883100
2.2316-2.31130.28451850.237126912876100
2.3113-2.40390.28371390.226827642903100
2.4039-2.51320.26621420.215627542896100
2.5132-2.64570.35891300.22427512881100
2.6457-2.81140.27171220.227927832905100
2.8114-3.02840.24261200.21927722892100
3.0284-3.33290.30911220.224128092931100
3.3329-3.81480.24051650.194927622927100
3.8148-4.80440.22671270.157528152942100
4.8044-35.87840.17321480.17622881302999
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)
10.45550.1825-0.22420.1261-0.16620.11490.1223-0.0939-0.40.0332-0.1005-0.3104-0.06090.02140.00110.2898-0.0578-0.00990.3013-0.02330.3122-78.8346-45.214214.339
20.1250.23950.09720.43440.62540.1958-0.46460.24990.2468-0.46240.3590.155-0.20040.1219-0.0010.3694-0.1138-0.01770.40970.04820.3644-58.3951-27.78178.4488
3-0.0008-0.0033-0.00170.03390.01560.00630.44360.2947-0.20330.13870.4238-0.0686-0.2633-0.24780.00070.6254-0.0113-0.14690.76790.04850.6776-105.2984-48.37913.1352
40.05350.03030.07760.08580.06490.10680.0625-0.05730.4690.21640.021-0.3809-0.10130.05010.00030.33910.06390.01720.33290.0020.4816-38.6919-93.460717.291
50.8387-0.1969-0.37341.17280.43250.4174-0.4198-0.4030.1050.51110.4239-0.13040.09490.0682-0.00460.3360.0274-0.03920.35110.03140.2443-67.8638-57.381224.1215
60.36970.28990.26310.6319-0.16280.47950.0915-0.41441.0857-0.09460.2494-0.5188-0.1990.10350.01260.34960.0243-0.00310.3228-0.09970.5001-77.1843-40.087626.5417
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 74 through 167 )A74 - 167
2X-RAY DIFFRACTION2chain 'A' and (resid 168 through 230 )A168 - 230
3X-RAY DIFFRACTION3chain 'A' and (resid 231 through 239 )A231 - 239
4X-RAY DIFFRACTION4chain 'B' and (resid 74 through 92 )B74 - 92
5X-RAY DIFFRACTION5chain 'B' and (resid 93 through 166 )B93 - 166
6X-RAY DIFFRACTION6chain 'B' and (resid 167 through 230 )B167 - 230

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