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- PDB-7w6b: Crystal Structure of PitA from pilus islet-2 of Streptococcus oralis -
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Open data
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Basic information
Entry | Database: PDB / ID: 7w6b | ||||||
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Title | Crystal Structure of PitA from pilus islet-2 of Streptococcus oralis | ||||||
![]() | von Willebrand factor type A domain protein | ||||||
![]() | CELL ADHESION / Tip pilin / adhesin / PitA / PI-2 pilus / Streptococcus oralis / isopeptide / CnaA fold / CnaB fold / vWFA fold / dental plaque / biofilm | ||||||
Function / homology | Domain of unknown function DUF5979 / Domain of unknown function (DUF5979) / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / membrane / IODIDE ION / von Willebrand factor type A domain protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yadav, R.K. / Krishnan, V. | ||||||
Funding support | ![]()
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![]() | ![]() Title: New structural insights into the PI-2 pilus from Streptococcus oralis, an early dental plaque colonizer. Authors: Yadav, R.K. / Krishnan, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 288.9 KB | Display | ![]() |
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PDB format | ![]() | 225.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439 KB | Display | ![]() |
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Full document | ![]() | 455.6 KB | Display | |
Data in XML | ![]() | 29.1 KB | Display | |
Data in CIF | ![]() | 39.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7f7yC ![]() 7vcnC ![]() 7vcrSC ![]() 7w7iC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 88094.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: HMPREF8579_1184 / Production host: ![]() ![]() | ||||||
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#2: Chemical | ChemComp-MG / | ||||||
#3: Chemical | ChemComp-IOD / #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.48 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 100 mM HEPES pH 7.8, 1 M potassium iodide, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7712 Å / Relative weight: 1 |
Reflection | Resolution: 2.984→51.93 Å / Num. obs: 20771 / % possible obs: 95 % / Redundancy: 7 % / CC1/2: 0.991 / Rpim(I) all: 0.072 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.984→3.068 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1039 / CC1/2: 0.577 / Rpim(I) all: 0.479 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7VCR Resolution: 2.984→51.93 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.807 / WRfactor Rfree: 0.284 / WRfactor Rwork: 0.242 / SU B: 39.76 / SU ML: 0.391 / Average fsc free: 0 / Average fsc work: 0 / Cross valid method: FREE R-VALUE / ESU R Free: 0.526 / Details: Hydrogens have not been used
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 85.705 Å2
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Refinement step | Cycle: LAST / Resolution: 2.984→51.93 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -11.7668 Å / Origin y: 68.6396 Å / Origin z: -1.9585 Å
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Refinement TLS group | Selection: ALL |