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- PDB-5nfi: The fimbrial anchor protein Mfa2 from Porphyromonas gingivalis -

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Basic information

Entry
Database: PDB / ID: 5nfi
TitleThe fimbrial anchor protein Mfa2 from Porphyromonas gingivalis
ComponentsMinor fimbrium anchoring subunit Mfa2
KeywordsCELL ADHESION / FIMBRIA / ADHESIN / PERIODONTITIS
Function / homology
Function and homology information


pilus assembly / cell outer membrane
Similarity search - Function
Immunoglobulin-like - #2090 / Immunoglobulin-like - #2100 / Fimbrium subunit FimB/Mfa2/Mfa3 / Fimbrillin-A associated anchor proteins Mfa1 and Mfa2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Minor fimbrium anchoring subunit Mfa2
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.508 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 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 2.0Nov 20, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _atom_site.occupancy / _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
B: Minor fimbrium anchoring subunit Mfa2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2073
Polymers31,9531
Non-polymers2542
Water48627
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-1 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.600, 83.210, 38.740
Angle α, β, γ (deg.)90.000, 94.760, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-516-

HOH

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Components

#1: Protein Minor fimbrium anchoring subunit Mfa2 / Minor fimbrial antigen 2


Mass: 31953.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MKHHHHHHPMSDYDIPTTENLYFQGAMDKMIYDNYDDCPRGVYVNFYS QTECAENPSYPAEVARLNVYAFDKDGILRSANVFEDVQLSAAKEWLIPLEKDGLYTIFAW GNIDDHYNIGEIKIGETTKQQVLMRLKQDGKWATNIDGTTLWYATSPVVELKNMEDGADQ ...Details: MKHHHHHHPMSDYDIPTTENLYFQGAMDKMIYDNYDDCPRGVYVNFYS QTECAENPSYPAEVARLNVYAFDKDGILRSANVFEDVQLSAAKEWLIPLEKDGLYTIFAW GNIDDHYNIGEIKIGETTKQQVLMRLKQDGKWATNIDGTTLWYATSPVVELKNMEDGADQ YIHTRANLREYTNRVTVSVDSLPHPENYEIKLASSNGSYRFDGTVAKADSTYYPGETKVV GDSTCRAFFTTLKLESGHENTLSVTHKPTGREIFRTDLVGAILSGQYAQNINLRCINDFDIRLVAHHCNC PDDTYVVVQIWINGWLIHSYEIEL
Source: (gene. exp.) Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561) (bacteria)
Strain: ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561
Gene: mfa2, PGN_0288 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2RHG2
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis-Tris propane pH 7.0, 20%, PEG 3350 and 0.2 M sodium iodide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 2.508→41.605 Å / Num. obs: 11043 / % possible obs: 99.6 % / Redundancy: 12.7 % / Biso Wilson estimate: 53.28 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.033 / Net I/σ(I): 14.7
Reflection shellResolution: 2.508→2.61 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.832 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1236 / CC1/2: 0.664 / Rpim(I) all: 0.408 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.508→41.605 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.78
RfactorNum. reflection% reflection
Rfree0.2626 529 4.79 %
Rwork0.1966 --
obs0.1997 11041 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 134.58 Å2 / Biso mean: 64.241 Å2 / Biso min: 35.33 Å2
Refinement stepCycle: final / Resolution: 2.508→41.605 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2213 0 2 27 2242
Biso mean--56.31 53.42 -
Num. residues----277
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082267
X-RAY DIFFRACTIONf_angle_d1.2183084
X-RAY DIFFRACTIONf_chiral_restr0.045342
X-RAY DIFFRACTIONf_plane_restr0.005398
X-RAY DIFFRACTIONf_dihedral_angle_d14.85811
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5081-2.76040.35351210.30252598271999
2.7604-3.15980.3281280.243426192747100
3.1598-3.98050.27031450.194526192764100
3.9805-41.61070.22641350.165626762811100
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)
11.4172-0.21540.23843.35391.5381.95880.0156-0.19690.21380.11220.0959-0.2613-0.2138-0.0049-0.13590.5955-0.02520.02620.5603-0.00780.540635.415834.599310.324
22.88430.35550.11653.81170.8221.50510.1115-0.19-0.32030.27440.1461-0.42770.17430.0006-0.2770.4675-0.0086-0.00140.54070.0240.451939.32137.1534.6438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain B and resid 40:222)B40 - 222
2X-RAY DIFFRACTION2(chain B and resid 223:320)B223 - 320

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