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- PDB-5ke1: Structure of a C-terminal fragment of the IcsA/VirG passenger-domain -

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Basic information

Entry
Database: PDB / ID: 5ke1
TitleStructure of a C-terminal fragment of the IcsA/VirG passenger-domain
ComponentsOuter membrane protein IcsA autotransporter
KeywordsTRANSPORT PROTEIN / virulence factor / autochaperone / autotransporter
Function / homology
Function and homology information


cell tip / cell outer membrane / periplasmic space / cell adhesion / cell surface / extracellular region
Similarity search - Function
Autochaperone Domain Type 1 / Autochaperone domain type 1 / : / Autotransporter-associated beta strand repeat / Passenger-associated-transport-repeat / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain ...Autochaperone Domain Type 1 / Autochaperone domain type 1 / : / Autotransporter-associated beta strand repeat / Passenger-associated-transport-repeat / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / Autotransporter, pectate lyase C-like domain superfamily / Pectin lyase fold/virulence factor
Similarity search - Domain/homology
NICKEL (II) ION / Outer membrane autotransporter IcsA
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLeupold, S. / Scrima, A.
Funding support Germany, France, 5items
OrganizationGrant numberCountry
Helmholtz AssociationVH-NG-727 Germany
BioStruct-X283570 Germany
Grenoble Instruct CenterUMS 3518 CNRS-CEA-UJF-EMBL France
FRISBIANR-10-INSB-05-02 France
GRALANR-10-LABX-49-01 France
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Structural insights into the architecture of the Shigella flexneri virulence factor IcsA/VirG and motifs involved in polar distribution and secretion.
Authors: Leupold, S. / Busing, P. / Mas, P.J. / Hart, D.J. / Scrima, A.
History
DepositionJun 9, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane protein IcsA autotransporter
B: Outer membrane protein IcsA autotransporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2623
Polymers73,2032
Non-polymers591
Water8,341463
1
A: Outer membrane protein IcsA autotransporter


Theoretical massNumber of molelcules
Total (without water)36,6021
Polymers36,6021
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer membrane protein IcsA autotransporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6602
Polymers36,6021
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.870, 84.670, 114.270
Angle α, β, γ (deg.)90.000, 98.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Outer membrane protein IcsA autotransporter


Mass: 36601.578 Da / Num. of mol.: 2 / Fragment: UNP residues 419-758
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: icsA, virG, CP0182 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7BCK4
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 0.2 M KCl, 0.1 M TRIS pH 7.2, 26% Jeffamine M-2070

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.9→42.335 Å / Num. obs: 52462 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Net I/σ(I): 13.11
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.9-20.8172.5197.6
2-2.10.5483.65198
2.1-2.20.4165.06197.9
2.2-2.50.2677.39198.1
2.5-30.12413.6198.9
3-60.05129.18199.2
6-100.03536.49199.9
100.02642198.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ML3

3ml3


Resolution: 1.9→42.335 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.81
RfactorNum. reflection% reflection
Rfree0.195 2623 5 %
Rwork0.1664 --
obs0.1679 52451 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.8 Å2 / Biso mean: 47.339 Å2 / Biso min: 16.98 Å2
Refinement stepCycle: final / Resolution: 1.9→42.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4775 0 1 463 5239
Biso mean--19.75 42.69 -
Num. residues----641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054845
X-RAY DIFFRACTIONf_angle_d0.6936577
X-RAY DIFFRACTIONf_chiral_restr0.052778
X-RAY DIFFRACTIONf_plane_restr0.004847
X-RAY DIFFRACTIONf_dihedral_angle_d9.7732855
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.93450.27531350.2632549268497
1.9345-1.97170.28141370.24392603274098
1.9717-2.0120.28031380.23662622276098
2.012-2.05570.23181350.21782562269798
2.0557-2.10350.2481380.20682638277698
2.1035-2.15610.24761360.19642578271498
2.1561-2.21440.26161370.18562593273098
2.2144-2.27960.21741360.1872594273098
2.2796-2.35310.22561380.1722614275298
2.3531-2.43720.22571370.17292611274898
2.4372-2.53480.1951390.17162637277699
2.5348-2.65020.23091380.17742624276299
2.6502-2.78990.1911400.17522655279599
2.7899-2.96460.22841390.17342636277599
2.9646-3.19340.20311370.17162618275599
3.1934-3.51470.19571400.16412659279999
3.5147-4.02290.16971410.14542665280699
4.0229-5.06710.12861390.122658279799
5.0671-42.34550.16581430.15292712285599
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)
10.7746-0.5442.99470.0943-1.42279.0212-0.08540.14320.0968-0.1901-0.00760.1908-0.3328-0.30550.040.3937-0.0044-0.05430.75680.08060.3521-5.118418.9813-13.1684
21.4271-0.891.40021.109-0.68285.209-0.08780.88510.4313-0.1595-0.2701-0.2178-0.41080.57730.27410.3697-0.0871-0.03680.78280.21930.34817.313318.7537-4.3875
33.0024-0.80052.3921.9137-1.08994.02660.12910.3728-0.0481-0.297-0.07510.0710.4020.0618-0.05140.2184-0.0276-0.00850.32920.00730.153211.92356.759315.7239
42.11211.3610.2623.5052-2.81844.4398-0.02560.2187-0.4824-0.49710.2821-0.07440.7674-0.4355-0.2590.3125-0.0568-0.03610.3028-0.01550.250315.953-5.163227.8159
54.09431.14120.38514.8135-1.40610.56690.0739-0.1199-0.22910.06520.20960.50680.1859-0.2979-0.27030.299-0.1329-0.01230.39270.01430.177312.2361-1.867634.0894
64.09662.1671-1.66715.8379-1.8942.21320.1857-0.4541-0.01450.2605-0.04370.35990.1304-0.259-0.15580.195-0.0626-0.03490.33110.0410.161716.50062.43933.5972
75.79492.70160.00677.4602-3.98672.52490.4773-1.00610.10190.5892-0.24840.19850.0434-0.0092-0.17380.3615-0.1391-0.05740.40330.01740.173218.0595-3.181738.5361
84.0368-1.68764.25933.5083-3.93996.01180.3018-0.4515-0.31980.1324-0.05010.1510.2038-0.466-0.11130.41680.0862-0.11470.5563-0.05010.29187.258715.473483.3227
92.72410.37710.46151.5654-0.17826.4606-0.0352-0.5713-0.21110.33410.0607-0.10610.7661-0.0321-0.05380.39990.0944-0.04010.3716-0.00540.23660.981711.583869.4332
101.94210.29570.46041.65760.09365.2474-0.1015-0.13420.31390.0690.1181-0.0734-0.15310.0536-0.0190.1530.0108-0.01940.1897-0.03150.22660.16122.072546.7549
112.5740.6262-0.06726.3251-0.31813.524-0.16460.40430.7313-0.45390.04210.039-0.88480.00210.0480.3917-0.0256-0.06130.28060.09960.3849-3.028431.223728.5093
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 419 through 468 )A419 - 468
2X-RAY DIFFRACTION2chain 'A' and (resid 469 through 546 )A469 - 546
3X-RAY DIFFRACTION3chain 'A' and (resid 547 through 652 )A547 - 652
4X-RAY DIFFRACTION4chain 'A' and (resid 653 through 669 )A653 - 669
5X-RAY DIFFRACTION5chain 'A' and (resid 670 through 691 )A670 - 691
6X-RAY DIFFRACTION6chain 'A' and (resid 692 through 715 )A692 - 715
7X-RAY DIFFRACTION7chain 'A' and (resid 716 through 740 )A716 - 740
8X-RAY DIFFRACTION8chain 'B' and (resid 422 through 450 )B422 - 450
9X-RAY DIFFRACTION9chain 'B' and (resid 451 through 546 )B451 - 546
10X-RAY DIFFRACTION10chain 'B' and (resid 547 through 652 )B547 - 652
11X-RAY DIFFRACTION11chain 'B' and (resid 653 through 740 )B653 - 740

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