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- PDB-5dhm: Crystal structure of the fimbrial protein Mfa4 from Porphyromonas... -

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Basic information

Entry
Database: PDB / ID: 5dhm
TitleCrystal structure of the fimbrial protein Mfa4 from Porphyromonas gingivalis
Components(Immunoreactive 32 kDa antigen) x 2
KeywordsCELL ADHESION / Fimbria / adhesin / periodontitis
Function / homology
Function and homology information


pilus / cell outer membrane
Similarity search - Function
Minor fimbrium tip subunit MfA4, C-terminal / Immunoglobulin-like - #2580 / Major fimbrial subunit protein, N-terminal / Major fimbrial subunit protein (FimA) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Minor fimbrium tip subunit MfA4
Similarity search - Component
Biological speciesPorphyromonas gingivalis ATCC 33277 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsKloppsteck, P. / Hall, M. / Persson, K.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2011-4186 Sweden
Umea Centre for Microbial Research Sweden
CitationJournal: Sci Rep / Year: 2016
Title: Structure of the fimbrial protein Mfa4 from Porphyromonas gingivalis in its precursor form: implications for a donor-strand complementation mechanism.
Authors: Kloppsteck, P. / Hall, M. / Hasegawa, Y. / Persson, K.
History
DepositionAug 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: Immunoreactive 32 kDa antigen
C: Immunoreactive 32 kDa antigen
B: Immunoreactive 32 kDa antigen
D: Immunoreactive 32 kDa antigen


Theoretical massNumber of molelcules
Total (without water)75,9054
Polymers75,9054
Non-polymers00
Water3,333185
1
A: Immunoreactive 32 kDa antigen
C: Immunoreactive 32 kDa antigen


Theoretical massNumber of molelcules
Total (without water)37,9532
Polymers37,9532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-16 kcal/mol
Surface area14100 Å2
MethodPISA
2
B: Immunoreactive 32 kDa antigen
D: Immunoreactive 32 kDa antigen


Theoretical massNumber of molelcules
Total (without water)37,9532
Polymers37,9532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-17 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.683, 84.536, 138.364
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Immunoreactive 32 kDa antigen


Mass: 6464.676 Da / Num. of mol.: 2 / Fragment: UNP residues 26-51
Source method: isolated from a genetically manipulated source
Details: Cleaved by chymotrypsin from full-length molecule.
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Gene: PGN_0290 / Plasmid: His1a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: B2RHG4
#2: Protein Immunoreactive 32 kDa antigen


Mass: 31487.947 Da / Num. of mol.: 2 / Fragment: UNP residues 52-333
Source method: isolated from a genetically manipulated source
Details: Cleaved by chymotrypsin from full-length molecule.
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Gene: PGN_0290 / Plasmid: His1a / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: B2RHG4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 5% polyglutamic acid (PGA), 20% PEG4000 and 0.1 M Tris pH 8.0. Protein was treated with a-chymotrypsin before crystallization.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.973 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 1.9→84.54 Å / Num. all: 51290 / Num. obs: 327588 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 16
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 3.4 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→53.539 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2295 2614 5.1 %Random
Rwork0.1835 ---
obs0.1859 51209 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→53.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4598 0 0 185 4783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084690
X-RAY DIFFRACTIONf_angle_d1.1246382
X-RAY DIFFRACTIONf_dihedral_angle_d12.5461723
X-RAY DIFFRACTIONf_chiral_restr0.042738
X-RAY DIFFRACTIONf_plane_restr0.005814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8979-1.93240.29911300.24642378X-RAY DIFFRACTION94
1.9324-1.96960.30531250.23642542X-RAY DIFFRACTION100
1.9696-2.00980.28951480.22292511X-RAY DIFFRACTION99
2.0098-2.05350.21971460.20822505X-RAY DIFFRACTION100
2.0535-2.10130.22031280.20212572X-RAY DIFFRACTION100
2.1013-2.15380.26751200.20342512X-RAY DIFFRACTION100
2.1538-2.21210.25511560.19392531X-RAY DIFFRACTION100
2.2121-2.27720.24291490.19842569X-RAY DIFFRACTION100
2.2772-2.35070.27941380.2062534X-RAY DIFFRACTION100
2.3507-2.43470.24081360.20312525X-RAY DIFFRACTION100
2.4347-2.53220.26351400.20642553X-RAY DIFFRACTION100
2.5322-2.64740.27421410.20532578X-RAY DIFFRACTION100
2.6474-2.7870.24551480.21262531X-RAY DIFFRACTION100
2.787-2.96160.30291250.20542583X-RAY DIFFRACTION100
2.9616-3.19020.23891300.20692564X-RAY DIFFRACTION99
3.1902-3.51120.2051350.18592587X-RAY DIFFRACTION100
3.5112-4.01910.2121440.17182623X-RAY DIFFRACTION100
4.0191-5.06310.18331270.13142631X-RAY DIFFRACTION99
5.0631-53.56020.19951480.16742766X-RAY DIFFRACTION99
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)
10.9337-0.2927-0.24832.87850.1780.6768-0.1318-0.0217-0.09770.10180.06430.08360.1514-0.01330.06310.19190.00360.02540.2614-0.00770.171833.17411.7436146.6247
20.68111.28140.05514.95830.11580.9142-0.13820.0530.0139-0.66360.15250.3790.0826-0.0261-0.00470.3059-0.0912-0.07160.32160.02590.287241.7221-13.2568112.2309
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1((chain A and resid 24:51) and (chain C and resid 52-333))
2X-RAY DIFFRACTION2((chain B and resid 31:51) and (chain D and resid 53:333))

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