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- PDB-3hrv: Crystal structure of TcpA, a Type IV pilin from Vibrio cholerae E... -

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Basic information

Entry
Database: PDB / ID: 3hrv
TitleCrystal structure of TcpA, a Type IV pilin from Vibrio cholerae El Tor biotype
ComponentsToxin coregulated pilin
KeywordsCELL ADHESION / Type IV pili / pilin / Vibrio cholerae / toxin-coregulated pilus / microcolonies / colonization / virulence factor
Function / homology
Function and homology information


extracellular organelle / protein secretion by the type II secretion system / type II protein secretion system complex / 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 / molecular replacement / Resolution: 1.5 Å
AuthorsCraig, L. / Arvai, A.S. / Tainer, J.A.
CitationJournal: Mol.Microbiol. / Year: 2010
Title: Vibrio cholerae El Tor TcpA crystal structure and mechanism for pilus-mediated microcolony formation.
Authors: Lim, M.S. / Ng, D. / Zong, Z. / Arvai, A.S. / Taylor, R.K. / Tainer, J.A. / Craig, L.
History
DepositionJun 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: 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 1.4Nov 20, 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 pilin
B: Toxin coregulated pilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0498
Polymers39,4842
Non-polymers5646
Water8,323462
1
A: Toxin coregulated pilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0224
Polymers19,7421
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Toxin coregulated pilin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0264
Polymers19,7421
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.767, 94.752, 128.422
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-832-

HOH

21A-861-

HOH

31B-431-

HOH

41B-651-

HOH

51B-661-

HOH

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Components

#1: Protein Toxin coregulated pilin / TcpA / Toxin-coregulated pilus subunit


Mass: 19742.086 Da / Num. of mol.: 2 / Fragment: globular domain, residues 29-199
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: El Tor H1 / Gene: tcpA / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B / References: UniProt: Q60153
#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: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.42 Å3/Da / Density % sol: 49.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Na-HEPES, 1.5 M LiSO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 7, 2003
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 23.75 / Number: 420254 / Rmerge(I) obs: 0.068 / Χ2: 1.02 / D res high: 1.5 Å / D res low: 20 Å / Num. obs: 61281 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
3.232096.210.0640.994
2.563.2398.710.0590.853
2.242.5699.410.0670.943
2.042.2499.610.0680.895
1.892.0499.810.0830.986
1.781.8999.910.1171.136
1.691.7899.910.1681.133
1.621.6999.910.2271.126
1.551.6299.910.3061.131
1.51.5510010.4131.078
ReflectionResolution: 1.5→20 Å / Num. all: 61737 / Num. obs: 61281 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Χ2: 1.02 / Net I/σ(I): 23.746
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 4.95 / Num. unique all: 6084 / Rsym value: 0.413 / Χ2: 1.078 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OQV

1oqv


Resolution: 1.5→20 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.78 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 5963 9.7 %random
Rwork0.219 52667 --
obs-58630 95.3 %-
Solvent computationBsol: 54.087 Å2
Displacement parametersBiso max: 80.36 Å2 / Biso mean: 25.47 Å2 / Biso min: 10.28 Å2
Baniso -1Baniso -2Baniso -3
1-2.187 Å20 Å20 Å2
2---6.819 Å20 Å2
3---4.632 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.227 Å0.216 Å
Luzzati d res low-5 Å
Luzzati sigma a0.217 Å0.202 Å
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2458 0 33 462 2953
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1741.5
X-RAY DIFFRACTIONc_scbond_it1.9392
X-RAY DIFFRACTIONc_mcangle_it1.6832
X-RAY DIFFRACTIONc_scangle_it2.5242.5
LS refinement shell
Resolution (Å)Rfactor RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.5-1.550.33310.3095X-RAY DIFFRACTION6084100
1.55-1.620.29290.2852X-RAY DIFFRACTION610799.9
1.62-1.690.26690.2634X-RAY DIFFRACTION611999.9
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param
X-RAY DIFFRACTION3so4.param
X-RAY DIFFRACTION4gol.param

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