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- PDB-6to1: Crystal structure of three N-terminal domains of the type V pili ... -

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Basic information

Entry
Database: PDB / ID: 6to1
TitleCrystal structure of three N-terminal domains of the type V pili tip protein Mfa5 from Porphyromonas gingivalis
ComponentsMinor fimbrium subunit Mfa5
KeywordsCELL ADHESION / Intramolekular Isopeptide / von Willebrand factor / Bacterial adhesion / P. gingivalis / Mfa1 fimbriae / Type V pili
Function / homologyvon Willebrand factor type A domain / pilus / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / PHOSPHATE ION / Minor fimbrium subunit Mfa5
Function and homology information
Biological speciesPorphyromonas gingivalis ATCC 33277 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPersson, K. / Heidler, T.V.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Other privateKempestiftelserna Sweden
Swedish Research Council2016-05009 Sweden
CitationJournal: Commun Biol / Year: 2021
Title: Porphyromonas gingivalis fimbrial protein Mfa5 contains a von Willebrand factor domain and an intramolecular isopeptide.
Authors: Heidler, T.V. / Ernits, K. / Ziolkowska, A. / Claesson, R. / Persson, K.
History
DepositionDec 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Minor fimbrium subunit Mfa5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,7886
Polymers112,4391
Non-polymers3495
Water10,917606
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-43 kcal/mol
Surface area25280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.720, 72.810, 184.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Minor fimbrium subunit Mfa5


Mass: 112438.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GAM = expression Tag Remaining amino acids are 21-1044 of Mfa5
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Gene: PGN_0291 / Plasmid: pET / Details (production host): Hisx6_ZZ_GS_Tev / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: B2RHG5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 606 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.76 Å3/Da / Density % sol: 55.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 17% PEG3350, 80mM NaPO4 pH6, 3mM CaCL and 3mM MgCL

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Data collection

DiffractionMean temperature: 290 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9756 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2016 / Details: Sagitally bended Si111 crystal
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 1.799→46.98 Å / Num. obs: 64113 / % possible obs: 99.45 % / Redundancy: 13.1 % / Biso Wilson estimate: 23.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09715 / Rpim(I) all: 0.02756 / Rrim(I) all: 0.1011 / Net I/σ(I): 19.66
Reflection shellResolution: 1.799→1.863 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.126 / Mean I/σ(I) obs: 1.87 / Num. unique obs: 6117 / CC1/2: 0.646 / Rpim(I) all: 0.3445 / Rrim(I) all: 1.18 / % possible all: 95.94

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Processing

Software
NameVersionClassification
PHENIX1.14_3228refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TNJ

6tnj


Resolution: 1.8→46.98 Å / SU ML: 0.1642 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.1022
RfactorNum. reflection% reflection
Rfree0.1998 3206 5 %
Rwork0.161 --
obs0.1629 64105 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.21 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4351 0 17 606 4974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01084596
X-RAY DIFFRACTIONf_angle_d0.98496300
X-RAY DIFFRACTIONf_chiral_restr0.0601711
X-RAY DIFFRACTIONf_plane_restr0.0072826
X-RAY DIFFRACTIONf_dihedral_angle_d3.94463687
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.28151280.25272440X-RAY DIFFRACTION92.21
1.83-1.850.27371360.23012580X-RAY DIFFRACTION98.87
1.85-1.880.24331380.21212623X-RAY DIFFRACTION99.32
1.88-1.920.27211370.19622593X-RAY DIFFRACTION99.78
1.92-1.950.21541390.18862649X-RAY DIFFRACTION99.79
1.95-1.990.24961360.18142581X-RAY DIFFRACTION99.78
1.99-2.030.23731410.17352679X-RAY DIFFRACTION99.86
2.03-2.070.1981360.16082584X-RAY DIFFRACTION99.93
2.07-2.120.20421380.16412632X-RAY DIFFRACTION99.86
2.12-2.180.19721390.15532632X-RAY DIFFRACTION99.86
2.18-2.230.21321390.15712647X-RAY DIFFRACTION99.93
2.23-2.30.20671390.15252630X-RAY DIFFRACTION99.96
2.3-2.370.22341380.14712636X-RAY DIFFRACTION100
2.37-2.460.16481400.14892644X-RAY DIFFRACTION99.96
2.46-2.560.2081400.15022667X-RAY DIFFRACTION99.93
2.56-2.670.20191400.14952662X-RAY DIFFRACTION99.75
2.67-2.820.2111400.15372665X-RAY DIFFRACTION100
2.82-2.990.19191400.15412660X-RAY DIFFRACTION99.96
2.99-3.220.18841410.15172666X-RAY DIFFRACTION99.82
3.22-3.550.17291410.14982690X-RAY DIFFRACTION99.89
3.55-4.060.17361440.14772725X-RAY DIFFRACTION100
4.06-5.110.16481440.13892748X-RAY DIFFRACTION99.72
5.11-46.980.23951520.20232866X-RAY DIFFRACTION99.34

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