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- PDB-5nf3: The fimbrial shaft protein Mfa1 from Porphyromonas gingivalis-C-t... -

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Basic information

Entry
Database: PDB / ID: 5nf3
TitleThe fimbrial shaft protein Mfa1 from Porphyromonas gingivalis-C-terminal deletion
ComponentsMinor fimbrium subunit Mfa1
KeywordsCELL ADHESION / FIMBRIA / ADHESIN / PERIODONTITIS
Function / homologypilus shaft / Fimbrial subunit protein, C-terminal / Major fimbrial subunit protein type IV, Fimbrillin, C-terminal / outer membrane / cell outer membrane / cell-cell adhesion / Prokaryotic membrane lipoprotein lipid attachment site profile. / ACETATE ION / Minor fimbrium subunit Mfa1
Function and homology information
Biological speciesPorphyromonas gingivalis ATCC 33277 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsHall, M. / Hasegawa, Y. / Persson, K. / Yoshimura, F.
Funding support Sweden, Japan, 2items
OrganizationGrant numberCountry
Swedish Research Council2016-05009 Sweden
Japan Society for the Promotion of Science16K11466 Japan
CitationJournal: Sci Rep / Year: 2018
Title: Structural and functional characterization of shaft, anchor, and tip proteins of the Mfa1 fimbria from the periodontal pathogen Porphyromonas gingivalis.
Authors: Hall, M. / Hasegawa, Y. / Yoshimura, F. / Persson, K.
History
DepositionMar 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Minor fimbrium subunit Mfa1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6353
Polymers56,5361
Non-polymers992
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-1 kcal/mol
Surface area20740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.262, 66.262, 286.607
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-753-

HOH

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Components

#1: Protein Minor fimbrium subunit Mfa1 / Pg-II fim a


Mass: 56536.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Gene: mfa1, PGN_0287 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: B2RHG1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 8000, 75 mM calcium acetate, 0.1 M sodium cacodylate pH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.97→48.65 Å / Num. obs: 46649 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 25.76 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.061 / Rrim(I) all: 0.22 / Net I/σ(I): 14.9 / Num. measured all: 587519 / Scaling rejects: 1543
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
1.97-2.0413.21.7390.6910.4951.809100
7.63-48.65100.0630.9990.020.06699.7

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→48.648 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.51
RfactorNum. reflection% reflection
Rfree0.2195 2000 4.3 %
Rwork0.1786 --
obs0.1804 46513 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 169.35 Å2 / Biso mean: 36.3687 Å2 / Biso min: 13.33 Å2
Refinement stepCycle: final / Resolution: 1.97→48.648 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3788 0 8 300 4096
Biso mean--19.02 31.02 -
Num. residues----497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083880
X-RAY DIFFRACTIONf_angle_d1.0735292
X-RAY DIFFRACTIONf_chiral_restr0.043599
X-RAY DIFFRACTIONf_plane_restr0.006689
X-RAY DIFFRACTIONf_dihedral_angle_d11.6561412
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.97-2.01930.40121390.393831043243
2.0193-2.07390.33611420.342831233265
2.0739-2.13490.31361400.261631293269
2.1349-2.20380.28741390.215330953234
2.2038-2.28260.26651400.205131363276
2.2826-2.3740.25871400.202731103250
2.374-2.4820.22611410.178331323273
2.482-2.61290.21531420.161331503292
2.6129-2.77660.23291420.168931663308
2.7766-2.99090.19661420.172931753317
2.9909-3.29180.19121450.169632083353
3.2918-3.7680.22551440.163732113355
3.768-4.74670.16351480.129232833431
4.7467-48.66320.18381560.157834913647
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.56950.1982-0.80310.5641-0.75692.23430.0055-0.1817-0.05980.118-0.0957-0.1167-0.10130.39330.06350.2222-0.01840.0040.2854-0.00770.2426-29.03529.143829.8556
20.5280.1732-0.48170.4698-0.41132.1725-0.0050.0043-0.018-0.0198-0.0047-0.0272-0.00870.11070.00950.13950.0141-0.00170.1689-0.02960.2084-21.563715.5291-8.3216
30.79890.4963-0.34960.5863-0.42721.8953-0.07310.0402-0.0936-0.0602-0.0418-0.04090.22180.04560.08280.17970.00210.02560.1562-0.0180.1919-24.26649.8234-5.9409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 32:237)A32 - 237
2X-RAY DIFFRACTION2(chain A and resid 238:460)A238 - 460
3X-RAY DIFFRACTION3(chain A and resid 461:554)A461 - 554

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