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- PDB-3oc5: Crystal Structure of the vibrio cholerae secreted colonization fa... -

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Basic information

Entry
Database: PDB / ID: 3oc5
TitleCrystal Structure of the vibrio cholerae secreted colonization factor TcpF
ComponentsToxin coregulated pilus biosynthesis protein F
KeywordsCELL ADHESION / MULTIDOMAIN PROTEIN / immunoglobulin-like (Ig-like) fold
Function / homologyVibrio 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 / cell outer membrane / Immunoglobulin-like / Sandwich / Mainly Beta / Toxin coregulated pilus biosynthesis protein F
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 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 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toxin coregulated pilus biosynthesis protein F


Theoretical massNumber of molelcules
Total (without water)35,8831
Polymers35,8831
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Toxin coregulated pilus biosynthesis protein F
x 12


Theoretical massNumber of molelcules
Total (without water)430,59512
Polymers430,59512
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation28_544x,-y-1/2,-z-1/21
crystal symmetry operation32_544-z,x-1/2,-y-1/21
crystal symmetry operation36_544-y,-z-1/2,x-1/21
crystal symmetry operation51_554-x+1/2,y,-z-1/21
crystal symmetry operation54_554z+1/2,-x,-y-1/21
crystal symmetry operation57_554y+1/2,z,x-1/21
crystal symmetry operation74_545-x+1/2,-y-1/2,z1
crystal symmetry operation77_545z+1/2,x-1/2,y1
crystal symmetry operation83_545y+1/2,-z-1/2,-x1
Buried area23980 Å2
ΔGint-106 kcal/mol
Surface area149710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)224.880, 224.880, 224.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number209
Space group name H-MF432

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Components

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


Mass: 35882.938 Da / Num. of mol.: 1 / Fragment: UNP residues 21-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: tcpF, VC_0837 / Production host: Vibrio cholerae (bacteria) / References: UniProt: P0C6Q5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 3.3 Å3/Da / Density % sol: 62.74 %
Crystal growTemperature: 293 K / pH: 7.5
Details: (NH4)2 H PO4 1M, Imidazole 100 mM, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9116,0.9794
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 15, 2007
RadiationMonochromator: SI 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91161
20.97941
ReflectionResolution: 2.4→20 Å / Num. obs: 19524 / % possible obs: 99.4 % / Observed criterion σ(I): 2.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→19.65 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.904 / SU B: 14.281 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 2.3 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 977 5 %RANDOM
Rwork0.229 ---
obs0.23 18547 --
all-19532 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.62 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2149 0 0 132 2281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222214
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.131.9653011
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7625285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24224.46894
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36915332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.275158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211713
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5171.51418
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.97822261
X-RAY DIFFRACTIONr_scbond_it1.2913796
X-RAY DIFFRACTIONr_scangle_it2.1524.5750
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 68 -
Rwork0.317 1286 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 59.423 Å / Origin y: -38.2792 Å / Origin z: -15.7493 Å
111213212223313233
T0.0672 Å2-0.0558 Å2-0.0734 Å2-0.3089 Å20.1415 Å2--0.1623 Å2
L1.3979 °21.111 °2-0.0279 °2-2.4622 °2-0.7328 °2--1.3789 °2
S-0.1412 Å °0.0477 Å °0.1734 Å °-0.2633 Å °0.3911 Å °0.5952 Å °0.0539 Å °-0.5017 Å °-0.2499 Å °

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