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- PDB-7w64: Crystal structure of minor pilin TcpB from Vibrio cholerae comple... -

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Basic information

Entry
Database: PDB / ID: 7w64
TitleCrystal structure of minor pilin TcpB from Vibrio cholerae complexed with N-terminal peptide fragment of TcpF
Components
  • TcpF
  • Toxin-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 / MOLECULAR REPLACEMENT / Resolution: 2.3 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
Revision 1.3Nov 6, 2024Group: Structure summary / Category: 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
D: Toxin-coregulated pilus biosynthesis protein B
E: Toxin-coregulated pilus biosynthesis protein B
F: Toxin-coregulated pilus biosynthesis protein B
G: TcpF
H: TcpF
I: TcpF
J: TcpF
K: TcpF
L: TcpF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,87630
Polymers270,98412
Non-polymers89218
Water6,521362
1
A: Toxin-coregulated pilus biosynthesis protein B
B: Toxin-coregulated pilus biosynthesis protein B
C: Toxin-coregulated pilus biosynthesis protein B
G: TcpF
H: TcpF
I: TcpF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,07716
Polymers135,4926
Non-polymers58510
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25660 Å2
ΔGint-200 kcal/mol
Surface area48260 Å2
MethodPISA
2
D: Toxin-coregulated pilus biosynthesis protein B
E: Toxin-coregulated pilus biosynthesis protein B
F: Toxin-coregulated pilus biosynthesis protein B
J: TcpF
K: TcpF
L: TcpF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,79914
Polymers135,4926
Non-polymers3078
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25980 Å2
ΔGint-206 kcal/mol
Surface area48670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.883, 128.555, 327.242
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Protein/peptide , 2 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Toxin-coregulated pilus biosynthesis protein B


Mass: 43507.301 Da / Num. of mol.: 6
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/peptide
TcpF


Mass: 1656.661 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria)

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Non-polymers , 4 types, 380 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.95 Å3/Da / Density % sol: 58.33 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, 0.28 M CaCl2, 22%(v/v) PEG400, pH7.5

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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: 2.3→48.77 Å / Num. obs: 139539 / % possible obs: 99.1 % / Redundancy: 10.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.029 / Rrim(I) all: 0.089 / Net I/σ(I): 12.1 / Num. measured all: 1413980 / Scaling rejects: 2766
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
2.3-2.3410.41.0697196269300.8510.3511.128299.7
12.6-48.7780.03874699280.9980.0140.04128.394.9

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Processing

Software
NameVersionClassification
PHENIX1.19-4092refinement
XDSdata reduction
Aimless0.5.32data scaling
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7W63

7w63


Resolution: 2.3→37.2 Å / SU ML: 0.3552 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.6784
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.264 13776 9.9 %
Rwork0.2217 125440 -
obs0.2258 139216 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.53 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18768 0 33 362 19163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008819119
X-RAY DIFFRACTIONf_angle_d1.071825852
X-RAY DIFFRACTIONf_chiral_restr0.06382868
X-RAY DIFFRACTIONf_plane_restr0.0073392
X-RAY DIFFRACTIONf_dihedral_angle_d13.77186971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.34344570.32944192X-RAY DIFFRACTION99.53
2.33-2.350.35824680.30754176X-RAY DIFFRACTION99.7
2.35-2.380.35364650.30274119X-RAY DIFFRACTION99.31
2.38-2.410.35634900.28964176X-RAY DIFFRACTION99.7
2.41-2.440.3334370.294146X-RAY DIFFRACTION99.16
2.44-2.480.36924780.28944157X-RAY DIFFRACTION99.1
2.48-2.510.33344840.28824116X-RAY DIFFRACTION98.82
2.51-2.550.33654530.27564099X-RAY DIFFRACTION98.94
2.55-2.590.31214390.27344190X-RAY DIFFRACTION98.93
2.59-2.630.32894190.27664181X-RAY DIFFRACTION99.05
2.63-2.680.31464590.27314206X-RAY DIFFRACTION99
2.68-2.730.31494460.27594146X-RAY DIFFRACTION99.33
2.73-2.780.35964600.30034219X-RAY DIFFRACTION99.13
2.78-2.840.34564720.28384103X-RAY DIFFRACTION99.24
2.84-2.90.32094600.26674177X-RAY DIFFRACTION98.83
2.9-2.960.32644560.274152X-RAY DIFFRACTION98.78
2.97-3.040.30584510.26674189X-RAY DIFFRACTION98.77
3.04-3.120.31014500.26634186X-RAY DIFFRACTION98.66
3.12-3.210.29834580.2564117X-RAY DIFFRACTION97.99
3.21-3.320.30964410.26784161X-RAY DIFFRACTION98.02
3.32-3.440.2864580.23914156X-RAY DIFFRACTION98.27
3.44-3.570.26524490.22324195X-RAY DIFFRACTION97.95
3.57-3.730.24794720.22574140X-RAY DIFFRACTION98.02
3.74-3.930.26454610.2154181X-RAY DIFFRACTION98.14
3.93-4.180.22035050.20314164X-RAY DIFFRACTION98.44
4.18-4.50.24484430.18084205X-RAY DIFFRACTION98.18
4.5-4.950.22594610.17234202X-RAY DIFFRACTION97.33
4.95-5.670.20844500.17964233X-RAY DIFFRACTION98.13
5.67-7.130.22624650.19164327X-RAY DIFFRACTION98.46
7.13-37.20.20434690.17494429X-RAY DIFFRACTION96.55

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