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- PDB-1oqv: Structure of TcpA, the Type IV pilin subunit from the toxin co-re... -

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Basic information

Entry
Database: PDB / ID: 1oqv
TitleStructure of TcpA, the Type IV pilin subunit from the toxin co-regulated pilus of Vibrio cholerae classical biotype
Componentstoxin-coregulated pilus subunit
KeywordsCELL ADHESION / TcpA / Type IV pilin / pilin / pilus filament / Vibrio cholerae / fiber forming protein / adhesin / fimbriae
Function / homology
Function and homology information


extracellular organelle / pilus / membrane
Similarity search - Function
TcpA-like pilin / TcpA-like pilin / Toxin-coregulated pilus subunit TcpA / Toxin-coregulated pilus subunit TcpA / Prokaryotic N-terminal methylation site. / Prokaryotic N-terminal methylation motif / Prokaryotic N-terminal methylation site / Pilin-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Toxin coregulated pilin
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsCraig, L. / Tainer, J.A.
CitationJournal: Mol.Cell / Year: 2003
Title: Type IV Pilin Structure and Assembly: X-Ray and EM Analyses of Vibrio cholerae Toxin-Coregulated Pilus and Pseudomonas aeruginosa PAK Pilin
Authors: Craig, L. / Taylor, R.K. / Pique, M.E. / Adair, B.D. / Arvai, A.S. / Singh, M. / Lloyd, S.J. / Shin, D.S. / Getzoff, E.D. / Yeager, M. / Forest, K.T. / Tainer, J.A.
History
DepositionMar 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 3, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: toxin-coregulated pilus subunit
B: toxin-coregulated pilus subunit
C: toxin-coregulated pilus subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6596
Polymers59,3833
Non-polymers2763
Water13,781765
1
A: toxin-coregulated pilus subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8862
Polymers19,7941
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: toxin-coregulated pilus subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9783
Polymers19,7941
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: toxin-coregulated pilus subunit


Theoretical massNumber of molelcules
Total (without water)19,7941
Polymers19,7941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.317, 157.317, 35.719
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Detailsthousands of pilin subunits assemble to form a long thin filament 6 nm in diameter and several microns in length (see TCP model, PDB file XXX)

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Components

#1: Protein toxin-coregulated pilus subunit


Mass: 19794.285 Da / Num. of mol.: 3 / Fragment: globular head domain, residues 29-199
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: tcpa / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami / References: UniProt: P23024
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 765 / Source method: isolated from a natural source / Formula: H2O
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: 1.99 Å3/Da / Density % sol: 37.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 8000, imidazole, sodium chloride, glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
230 %PEG80001reservoir
30.1 Mimidazole1reservoirpH8.0
40.2 M1reservoirpH8.0NaCl
56 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.975913 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 26, 2001
RadiationMonochromator: single crystal Si(111) bent monochoromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975913 Å / Relative weight: 1
ReflectionResolution: 1.3→30 Å / Num. all: 573481 / Num. obs: 115573 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.71 % / Biso Wilson estimate: 12.5 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 5.1
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 1.8 / Num. unique all: 17071 / Rsym value: 0.245 / % possible all: 93.9
Reflection
*PLUS
Num. measured all: 573481
Reflection shell
*PLUS
% possible obs: 93.9 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
SHELXL-97refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1.8 A structure of N-terminally truncated, SeMet-labelled TcpA

Resolution: 1.3→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.174 6110 -random
Rwork0.116 ---
all0.117 115573 --
obs0.113 115573 5 %-
Refinement stepCycle: LAST / Resolution: 1.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3681 0 18 765 4464
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d2.1
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.3 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.1

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