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- PDB-7w65: Crystal structure of minor pilin TcpB from Vibrio cholerae comple... -

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Basic information

Entry
Database: PDB / ID: 7w65
TitleCrystal structure of minor pilin TcpB from Vibrio cholerae complexed with secreted protein TcpF
Components
  • Toxin coregulated pilus biosynthesis protein F
  • Toxin-coregulated pilus biosynthesis protein B
KeywordsCELL ADHESION / Type IVb pilus / Vibrio cholerae / Minor pilin.
Function / homologyVibrio cholerae toxin co-regulated pilus biosynthesis F / Vibrio cholerae toxin co-regulated pilus biosynthesis F, C-terminal / Vibrio cholerae toxin co-regulated pilus biosynthesis protein F / cell outer membrane / Toxin coregulated pilus biosynthesis protein F / Toxin-coregulated pilus biosynthesis protein B
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.05 Å
AuthorsOki, H. / Kawahara, K. / Iimori, M. / Imoto, Y. / Maruno, T. / Uchiyama, S. / Muroga, Y. / Yoshida, A. / Yoshida, T. / Ohkubo, T. ...Oki, H. / Kawahara, K. / Iimori, M. / Imoto, Y. / Maruno, T. / Uchiyama, S. / Muroga, Y. / Yoshida, A. / Yoshida, T. / Ohkubo, T. / Matsuda, S. / Iida, T. / Nakamura, S.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19K23866 Japan
Japan Society for the Promotion of Science (JSPS)20K16245 Japan
CitationJournal: Sci Adv / Year: 2022
Title: Structural basis for the toxin-coregulated pilus-dependent secretion of Vibrio cholerae colonization factor.
Authors: Oki, H. / Kawahara, K. / Iimori, M. / Imoto, Y. / Nishiumi, H. / Maruno, T. / Uchiyama, S. / Muroga, Y. / Yoshida, A. / Yoshida, T. / Ohkubo, T. / Matsuda, S. / Iida, T. / Nakamura, S.
History
DepositionDec 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toxin-coregulated pilus biosynthesis protein B
B: Toxin-coregulated pilus biosynthesis protein B
C: Toxin-coregulated pilus biosynthesis protein B
D: Toxin coregulated pilus biosynthesis protein F
E: Toxin coregulated pilus biosynthesis protein F
F: Toxin coregulated pilus biosynthesis protein F


Theoretical massNumber of molelcules
Total (without water)238,1716
Polymers238,1716
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, Three TcpF molecules bind to TcpB trimer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28030 Å2
ΔGint-133 kcal/mol
Surface area90600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)284.139, 284.139, 297.599
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

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Components

#1: Protein Toxin-coregulated pilus biosynthesis protein B


Mass: 43507.301 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: tcpB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AGX1
#2: Protein Toxin coregulated pilus biosynthesis protein F / TCP pilus biosynthesis protein TcpF


Mass: 35882.938 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: tcpF / Production host: Escherichia coli (E. coli) / References: UniProt: A5F383

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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: 7.28 Å3/Da / Density % sol: 83.11 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop
Details: 0.4 M trisodium citrate, 4%(w/v) PEG3350, 10%(w/v) xylitol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.05→49.21 Å / Num. obs: 57983 / % possible obs: 99.9 % / Redundancy: 19 % / CC1/2: 0.999 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.04 / Rrim(I) all: 0.175 / Net I/σ(I): 13.1 / Num. measured all: 1100587 / Scaling rejects: 33
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
4.05-4.1619.73.0728763544390.5330.7073.1531.3100
17.65-49.2110.90.0584477740.9990.0140.0524294.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHENIXv1.19.2-4092refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7W63

7w63


Resolution: 4.05→31.83 Å / SU ML: 0.6315 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.1153
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3008 5702 9.87 %
Rwork0.2742 52098 -
obs0.2768 57800 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 221.44 Å2
Refinement stepCycle: LAST / Resolution: 4.05→31.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16441 0 0 0 16441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003916778
X-RAY DIFFRACTIONf_angle_d0.736922732
X-RAY DIFFRACTIONf_chiral_restr0.04592508
X-RAY DIFFRACTIONf_plane_restr0.00422950
X-RAY DIFFRACTIONf_dihedral_angle_d14.12256130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.05-4.10.39492080.40661676X-RAY DIFFRACTION99.84
4.1-4.140.40441630.41331737X-RAY DIFFRACTION100
4.14-4.190.38162000.4011708X-RAY DIFFRACTION100
4.19-4.250.37321920.39271719X-RAY DIFFRACTION99.9
4.25-4.30.38871810.39071703X-RAY DIFFRACTION99.89
4.3-4.360.37392070.38191681X-RAY DIFFRACTION99.95
4.36-4.420.38952090.37931705X-RAY DIFFRACTION99.9
4.42-4.490.40081800.37991698X-RAY DIFFRACTION100
4.49-4.560.39921670.36631739X-RAY DIFFRACTION100
4.56-4.630.35461860.37541709X-RAY DIFFRACTION100
4.63-4.710.37432020.37661699X-RAY DIFFRACTION99.95
4.71-4.80.361960.36091710X-RAY DIFFRACTION100
4.8-4.890.37631860.35321728X-RAY DIFFRACTION99.95
4.89-4.990.38041850.34581724X-RAY DIFFRACTION99.95
4.99-5.10.36831930.33591710X-RAY DIFFRACTION100
5.1-5.220.39812130.35581708X-RAY DIFFRACTION100
5.22-5.350.3521830.32721725X-RAY DIFFRACTION100
5.35-5.490.3771780.34161742X-RAY DIFFRACTION99.95
5.49-5.650.33671870.33061730X-RAY DIFFRACTION99.95
5.65-5.830.35531820.34031736X-RAY DIFFRACTION99.95
5.83-6.040.33251580.32911775X-RAY DIFFRACTION99.95
6.04-6.280.31611960.32221726X-RAY DIFFRACTION100
6.28-6.560.30821970.31231738X-RAY DIFFRACTION100
6.56-6.910.31561860.30461761X-RAY DIFFRACTION100
6.91-7.330.31851930.27531752X-RAY DIFFRACTION99.95
7.33-7.890.28861970.27221770X-RAY DIFFRACTION100
7.89-8.670.26451990.23831764X-RAY DIFFRACTION100
8.67-9.890.24671860.18811805X-RAY DIFFRACTION100
9.89-12.340.18521940.16141821X-RAY DIFFRACTION99.65
12.35-31.830.24111980.19261899X-RAY DIFFRACTION98.87

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