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- PDB-5nf4: The tip fimbrial protein Mfa3 from Porphyromonas gingivalis with ... -

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Basic information

Entry
Database: PDB / ID: 5nf4
TitleThe tip fimbrial protein Mfa3 from Porphyromonas gingivalis with C-terminal truncation.
ComponentsMinor fimbrium tip subunit Mfa3
KeywordsCELL ADHESION / FIMBRIA / ADHESIN / PERIODONTITIS
Function / homologyFimbrium subunit FimB/Mfa2/Mfa3 / Fimbrillin-A associated anchor proteins Mfa1 and Mfa2 / pilus tip / pilus / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / FORMIC ACID / Minor fimbrium tip subunit Mfa3
Function and homology information
Biological speciesPorphyromonas gingivalis ATCC 33277 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.746 Å
AuthorsHall, M. / Hasegawa, Y. / Yoshimura, F. / Persson, K.
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 tip subunit Mfa3
B: Minor fimbrium tip subunit Mfa3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,7027
Polymers101,3712
Non-polymers3305
Water7,602422
1
A: Minor fimbrium tip subunit Mfa3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8283
Polymers50,6861
Non-polymers1422
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Minor fimbrium tip subunit Mfa3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8744
Polymers50,6861
Non-polymers1883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.183, 80.183, 116.022
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Minor fimbrium tip subunit Mfa3


Mass: 50685.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Gene: mfa3, PGN_0289 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2RHG3
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 422 / 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: 3.09 Å3/Da / Density % sol: 60.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 3% PGA, 8% PEG 8000, 0.3 M sodium formate, 0.12 M ammonium sulfate and 0.1 M sodium acetate, pH 5.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.721→69.441 Å / Num. all: 79050 / Num. obs: 79050 / % possible obs: 93.2 % / Redundancy: 1.7 % / Biso Wilson estimate: 33.63 Å2 / Rpim(I) all: 0.028 / Rrim(I) all: 0.043 / Rsym value: 0.032 / Net I/av σ(I): 9.7 / Net I/σ(I): 12.2 / Num. measured all: 134723
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.75-1.841.70.3652.10.3430.5020.36593.4
1.84-1.951.70.1754.50.1630.240.17592.3
1.95-2.091.70.0977.90.090.1330.09795.9
2.09-2.251.70.06111.70.0550.0830.06193.7
2.25-2.471.70.04315.30.0390.0590.04393.2
2.47-2.761.70.03417.90.0310.0460.03494.5
2.76-3.191.70.02820.20.0240.0370.02892.3
3.19-3.91.70.02720.50.0230.0360.02793.9
3.9-5.521.70.02621.10.0230.0350.02691.8
5.52-44.521.80.03316.20.0290.0440.03384.2

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementResolution: 1.746→44.52 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 19.54
RfactorNum. reflection% reflection
Rfree0.1773 6008 7.61 %
Rwork0.1484 --
obs0.1506 78991 93.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 195.4 Å2 / Biso mean: 53.3268 Å2 / Biso min: 25.24 Å2
Refinement stepCycle: final / Resolution: 1.746→44.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4712 0 25 422 5159
Biso mean--73.43 52.38 -
Num. residues----590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014848
X-RAY DIFFRACTIONf_angle_d1.2456585
X-RAY DIFFRACTIONf_chiral_restr0.053714
X-RAY DIFFRACTIONf_plane_restr0.007856
X-RAY DIFFRACTIONf_dihedral_angle_d13.2621770
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7461-1.76590.29521860.2992404259090
1.7659-1.78670.31532110.28282455266695
1.7867-1.80850.29632130.27322433264694
1.8085-1.83140.25292270.23992457268494
1.8314-1.85550.26642100.22542404261492
1.8555-1.88090.25961820.21922399258192
1.8809-1.90780.23441810.20082332251388
1.9078-1.93630.23251920.19582421261394
1.9363-1.96650.22162260.1922527275396
1.9665-1.99880.21212120.18072505271797
1.9988-2.03320.19352060.15822484269096
2.0332-2.07020.19831980.16372499269795
2.0702-2.110.22971620.1662556271895
2.11-2.15310.19311900.15892491268194
2.1531-2.19990.17661980.14932405260394
2.1999-2.25110.2121710.15242417258892
2.2511-2.30740.20072030.15362335253889
2.3074-2.36970.17512380.14412390262894
2.3697-2.43950.17411990.15212557275696
2.4395-2.51820.19622090.1472484269395
2.5182-2.60820.19381980.15162452265095
2.6082-2.71260.17872170.15082451266894
2.7126-2.8360.18831930.15292417261092
2.836-2.98550.18631900.15632326251689
2.9855-3.17250.1871880.16052501268995
3.1725-3.41740.19882230.15572439266294
3.4174-3.76120.18231940.14882454264894
3.7612-4.3050.13972060.12272374258091
4.305-5.42240.13552040.10772411261593
5.4224-44.53430.14221810.13412203238485
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)
10.6376-0.039-0.2040.62140.74483.9961-0.0706-0.10920.20040.02410.045-0.013-0.5583-0.07390.01320.3860.09420.01920.2668-0.04530.3661-6.955424.680222.0038
22.19120.4736-0.23262.2765-0.26381.613-0.04910.10620.2532-0.2716-0.0452-0.1402-0.30810.32740.08740.3759-0.03060.02110.26020.03710.268110.808523.2769-2.7774
30.67210.02830.1770.4571-0.40885.1518-0.03240.07270.1684-0.15790.02130.2333-0.3347-0.6414-0.00080.39090.0912-0.05070.30540.00660.4086-19.639816.5126-12.2587
42.04540.5691-0.14223.0037-0.23362.5131-0.0564-0.3198-0.040.2516-0.06240.52260.3323-0.74530.06020.2922-0.05930.10160.4522-0.03680.3548-25.5317-0.321912.7077
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 34:190)A33 - 190
2X-RAY DIFFRACTION2(chain A and resid 191:341)A191 - 341
3X-RAY DIFFRACTION3(chain B and resid 34:190)B33 - 190
4X-RAY DIFFRACTION4(chain B and resid 191:341)B191 - 341

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