[English] 日本語
Yorodumi- PDB-7w6b: Crystal Structure of PitA from pilus islet-2 of Streptococcus oralis -
+Open data
-Basic information
Entry | Database: PDB / ID: 7w6b | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of PitA from pilus islet-2 of Streptococcus oralis | ||||||
Components | von Willebrand factor type A domain protein | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Streptococcus oralis ATCC 35037 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.984 Å | ||||||
Authors | Yadav, R.K. / Krishnan, V. | ||||||
Funding support | India, 1items
| ||||||
Citation | Journal: Febs J. / Year: 2022 Title: New structural insights into the PI-2 pilus from Streptococcus oralis, an early dental plaque colonizer. Authors: Yadav, R.K. / Krishnan, V. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7w6b.cif.gz | 288.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7w6b.ent.gz | 225.3 KB | Display | PDB format |
PDBx/mmJSON format | 7w6b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7w6b_validation.pdf.gz | 439 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7w6b_full_validation.pdf.gz | 455.6 KB | Display | |
Data in XML | 7w6b_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 7w6b_validation.cif.gz | 39.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/7w6b ftp://data.pdbj.org/pub/pdb/validation_reports/w6/7w6b | HTTPS FTP |
-Related structure data
Related structure data | 7f7yC 7vcnC 7vcrSC 7w7iC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 88094.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus oralis ATCC 35037 (bacteria) Gene: HMPREF8579_1184 / Production host: Escherichia coli (E. coli) / References: UniProt: D4FSQ3 | ||||||
---|---|---|---|---|---|---|---|
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.48 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.7712 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.984→51.93 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -11.7668 Å / Origin y: 68.6396 Å / Origin z: -1.9585 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection: ALL |