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- PDB-6mic: Crystal Structure of the C-terminal half of the Vibrio cholerae m... -

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Basic information

Entry
Database: PDB / ID: 6mic
TitleCrystal Structure of the C-terminal half of the Vibrio cholerae minor pilin TcpB
ComponentsToxin co-regulated pilus biosynthesis protein B
KeywordsBIOSYNTHETIC PROTEIN / Effector domain / Minor pilin / Toxin co-regulated pilus / Vibrio cholerae
Function / homologyToxin co-regulated pilus biosynthesis protein B
Function and homology information
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.531 Å
AuthorsKolappan, S. / Craig, L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP125959 Canada
CitationJournal: J.Biol.Chem. / Year: 2019
Title: TheVibrio choleraeminor pilin TcpB mediates uptake of the cholera toxin phage CTX phi.
Authors: Gutierrez-Rodarte, M. / Kolappan, S. / Burrell, B.A. / Craig, L.
History
DepositionSep 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Toxin co-regulated pilus biosynthesis protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9454
Polymers19,6431
Non-polymers3023
Water2,540141
1
A: Toxin co-regulated pilus biosynthesis protein B
hetero molecules

A: Toxin co-regulated pilus biosynthesis protein B
hetero molecules

A: Toxin co-regulated pilus biosynthesis protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,83512
Polymers58,9283
Non-polymers9079
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area13310 Å2
ΔGint-102 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.290, 63.290, 236.291
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-685-

HOH

21A-716-

HOH

31A-734-

HOH

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Components

#1: Protein Toxin co-regulated pilus biosynthesis protein B


Mass: 19642.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (bacteria) / Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: tcpB, VC0395_A0354 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: A0A0H3AKH0
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: MPD, sodium chloride, sodium acetate / PH range: 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2018 / Details: Rh coated collimating mirror, K-B focusing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.53→78.8 Å / Num. obs: 26889 / % possible obs: 96.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 12.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.016 / Rrim(I) all: 0.033 / Χ2: 1.15 / Net I/σ(I): 26.9
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.091 / Mean I/σ(I) obs: 12.4 / Num. unique obs: 1366 / CC1/2: 0.989 / Rpim(I) all: 0.053 / Rrim(I) all: 0.105 / Χ2: 0.93 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QS4

4qs4


Resolution: 1.531→39.382 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1982 1342 4.99 %
Rwork0.1784 --
obs0.1794 26883 95.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.531→39.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 20 141 1384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081261
X-RAY DIFFRACTIONf_angle_d0.9911707
X-RAY DIFFRACTIONf_dihedral_angle_d15.527750
X-RAY DIFFRACTIONf_chiral_restr0.057197
X-RAY DIFFRACTIONf_plane_restr0.006218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.531-1.58580.18651380.18222606X-RAY DIFFRACTION99
1.5858-1.64930.17591520.17182558X-RAY DIFFRACTION99
1.6493-1.72430.23781320.18352445X-RAY DIFFRACTION93
1.7243-1.81520.19861500.17752595X-RAY DIFFRACTION99
1.8152-1.9290.19611410.17222576X-RAY DIFFRACTION98
1.929-2.07790.17811100.16922447X-RAY DIFFRACTION92
2.0779-2.2870.19471440.16692611X-RAY DIFFRACTION99
2.287-2.61780.1781300.17422478X-RAY DIFFRACTION93
2.6178-3.2980.21121190.18292631X-RAY DIFFRACTION97
3.298-39.39480.20681260.18592594X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 25.6022 Å / Origin y: -13.0031 Å / Origin z: 6.9252 Å
111213212223313233
T0.0863 Å2-0.0002 Å2-0.0062 Å2-0.0778 Å2-0.0051 Å2--0.0971 Å2
L0.2693 °2-0.0168 °20.0009 °2-0.2484 °2-0.129 °2--0.1367 °2
S-0.0298 Å °0.0057 Å °-0.0312 Å °-0.0142 Å °0.0155 Å °0.045 Å °-0.0938 Å °-0.0564 Å °0.0388 Å °
Refinement TLS groupSelection details: all

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