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- PDB-7w63: Crystal structure of minor pilin TcpB from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 7w63
TitleCrystal structure of minor pilin TcpB from Vibrio cholerae
ComponentsToxin-coregulated pilus biosynthesis protein B
KeywordsCELL ADHESION / Type IVb pilus / Vibrio cholerae / Minor pilin.
Function / homologyToxin-coregulated pilus biosynthesis protein B
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.32 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 1.2Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,78837
Polymers130,5223
Non-polymers3,26634
Water12,917717
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19940 Å2
ΔGint-100 kcal/mol
Surface area49420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.830, 170.830, 262.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-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: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 717 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.67 Å3/Da / Density % sol: 66.51 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl, 1.8 M Lithium Sulfate Monohydrate, pH8.8

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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: Dec 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→47.75 Å / Num. obs: 83755 / % possible obs: 100 % / Redundancy: 39 % / CC1/2: 0.999 / Rmerge(I) obs: 0.207 / Rpim(I) all: 0.034 / Rrim(I) all: 0.21 / Net I/σ(I): 15.3 / Num. measured all: 3267250 / Scaling rejects: 477
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
2.32-2.3640.62.27118348845220.8560.362.2991.9100
12.06-47.7528.60.08194516810.9990.0140.0813798.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHENIXv1.19.2-4158refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.32→23.37 Å / SU ML: 0.2748 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.0143
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2076 8472 10.13 %
Rwork0.1738 75167 -
obs0.1772 83639 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.65 Å2
Refinement stepCycle: LAST / Resolution: 2.32→23.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9114 0 170 717 10001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00919415
X-RAY DIFFRACTIONf_angle_d1.183412752
X-RAY DIFFRACTIONf_chiral_restr0.05321391
X-RAY DIFFRACTIONf_plane_restr0.0051647
X-RAY DIFFRACTIONf_dihedral_angle_d15.62193392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.350.31742770.24472481X-RAY DIFFRACTION99.96
2.35-2.370.3022510.2332471X-RAY DIFFRACTION99.89
2.37-2.40.27142750.22032490X-RAY DIFFRACTION100
2.4-2.430.27292840.21172471X-RAY DIFFRACTION99.93
2.43-2.470.27912930.21532446X-RAY DIFFRACTION99.93
2.47-2.50.28972630.22312495X-RAY DIFFRACTION100
2.5-2.530.26422850.21392471X-RAY DIFFRACTION100
2.53-2.570.27782790.21052498X-RAY DIFFRACTION100
2.57-2.610.26972470.20672520X-RAY DIFFRACTION100
2.61-2.660.28622770.21872500X-RAY DIFFRACTION99.96
2.66-2.70.27472880.21732460X-RAY DIFFRACTION100
2.7-2.750.25972910.2182484X-RAY DIFFRACTION100
2.75-2.80.23582840.20112469X-RAY DIFFRACTION100
2.8-2.860.24282820.19932484X-RAY DIFFRACTION99.96
2.86-2.920.22163150.19662455X-RAY DIFFRACTION100
2.92-2.990.23042850.19582491X-RAY DIFFRACTION99.96
2.99-3.060.25792820.20092495X-RAY DIFFRACTION100
3.06-3.150.23442770.19962480X-RAY DIFFRACTION100
3.15-3.240.23842990.19692504X-RAY DIFFRACTION100
3.24-3.340.22353050.1872467X-RAY DIFFRACTION100
3.34-3.460.1962380.17712545X-RAY DIFFRACTION100
3.46-3.60.19872590.16192530X-RAY DIFFRACTION100
3.6-3.760.18992520.15622551X-RAY DIFFRACTION100
3.76-3.960.17733030.14692519X-RAY DIFFRACTION100
3.96-4.210.16143010.13892475X-RAY DIFFRACTION100
4.21-4.530.15872740.13292548X-RAY DIFFRACTION100
4.53-4.980.15592830.12892558X-RAY DIFFRACTION100
4.98-5.70.17642850.1552566X-RAY DIFFRACTION100
5.7-7.140.20993130.18032584X-RAY DIFFRACTION100
7.14-23.370.19993250.18222659X-RAY DIFFRACTION99.8

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