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Open data
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Basic information
Entry | Database: PDB / ID: 5nfi | |||||||||
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Title | The fimbrial anchor protein Mfa2 from Porphyromonas gingivalis | |||||||||
![]() | Minor fimbrium anchoring subunit Mfa2 | |||||||||
![]() | CELL ADHESION / FIMBRIA / ADHESIN / PERIODONTITIS | |||||||||
Function / homology | Fimbrium subunit FimB/Mfa2/Mfa3 / Fimbrillin-A associated anchor proteins Mfa1 and Mfa2 / pilus assembly / : / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / IODIDE ION / Minor fimbrium anchoring subunit Mfa2![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Hall, M. / Hasegawa, Y. / Persson, K. / Yoshimura, F. | |||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.5 KB | Display | ![]() |
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PDB format | ![]() | 99.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.2 KB | Display | ![]() |
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Full document | ![]() | 426.9 KB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 15.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | 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.) ![]() Strain: ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561 Gene: mfa2, PGN_0288 / Production host: ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.83 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97239 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 134.58 Å2 / Biso mean: 64.241 Å2 / Biso min: 35.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.508→41.605 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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