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- PDB-3oc8: Crystal Structure of the C-terminal Domain of the Vibrio cholerae... -

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Basic information

Entry
Database: PDB / ID: 3oc8
TitleCrystal Structure of the C-terminal Domain of the Vibrio cholerae soluble colonization factor TcpF
ComponentsToxin coregulated pilus biosynthesis protein F
KeywordsCELL ADHESION / immunoglobulin-like fold
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
Vibrio cholerae toxin co-regulated pilus biosynthesis protein F, C-terminal domain / Vibrio cholerae toxin co-regulated pilus biosynthesis F / Vibrio cholerae toxin co-regulated pilus biosynthesis F, C-terminal / Vibrio cholerae toxin co-regulated pilus biosynthesis protein F / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Toxin coregulated pilus biosynthesis protein F
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsCraig, L. / Kolappan, S. / Yuen, A.S.W.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal Structure of the Vibrio cholerae Colonization Factor TcpF and Identification of a Functional Immunogenic Site.
Authors: Megli, C.J. / Yuen, A.S. / Kolappan, S. / Richardson, M.R. / Dharmasena, M.N. / Krebs, S.J. / Taylor, R.K. / Craig, L.
History
DepositionAug 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toxin coregulated pilus biosynthesis protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0667
Polymers15,5091
Non-polymers5576
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Toxin coregulated pilus biosynthesis protein F
hetero molecules

A: Toxin coregulated pilus biosynthesis protein F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,13214
Polymers31,0192
Non-polymers1,11312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area3470 Å2
ΔGint-23 kcal/mol
Surface area13600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.220, 80.300, 56.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Toxin coregulated pilus biosynthesis protein F / TCP pilus biosynthesis protein tcpF


Mass: 15509.472 Da / Num. of mol.: 1 / Fragment: UNP residues 206-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: tcpF, VC_0837 / Production host: Escherichia coli (E. coli) / References: UniProt: P0C6Q5
#2: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 1.6 M Ammonium Sulfate, 0.1 M MES pH 6.5, 10% v/v Dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONSSRL BL11-111.0722
2
Detector
TypeIDDetectorDate
MARMOSAIC 325 mm CCD1CCDAug 8, 2009
2
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SIDE SCATTERING BENT CUBE-ROOT I -BEAM SINGLE CRYSTALSINGLE WAVELENGTHMx-ray1
2ASYMMETRIC CUT 4.965 DEGS.x-ray1
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 8452 / % possible obs: 96.1 % / Observed criterion σ(I): 22.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OC5

3oc5


Resolution: 2.1→19.41 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.48 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.238 423 5 %RANDOM
Rwork0.169 ---
obs0.173 8029 --
all-8452 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20 Å2
2---0.48 Å20 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 34 108 1202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221134
X-RAY DIFFRACTIONr_bond_other_d0.0010.02751
X-RAY DIFFRACTIONr_angle_refined_deg1.8241.981536
X-RAY DIFFRACTIONr_angle_other_deg0.99331849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8595137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82825.650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66715186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg37.366151
X-RAY DIFFRACTIONr_chiral_restr0.1110.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211247
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02213
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8691.5677
X-RAY DIFFRACTIONr_mcbond_other0.2441.5276
X-RAY DIFFRACTIONr_mcangle_it1.56721099
X-RAY DIFFRACTIONr_scbond_it2.73457
X-RAY DIFFRACTIONr_scangle_it3.924.5437
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 24 -
Rwork0.169 447 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 18.0308 Å / Origin y: 15.166 Å / Origin z: -11.8731 Å
111213212223313233
T0.0345 Å2-0.0111 Å2-0.0154 Å2-0.0271 Å20.0101 Å2--0.0207 Å2
L1.8905 °2-0.7674 °2-0.2478 °2-0.83 °20.2676 °2--0.2985 °2
S0.0563 Å °0.063 Å °-0.1308 Å °-0.054 Å °-0.0394 Å °0.0865 Å °0.0397 Å °-0.0824 Å °-0.0169 Å °

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