[English] 日本語
Yorodumi- PDB-3doa: The crystal structure of the fibrinogen binding protein from Stap... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3doa | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of the fibrinogen binding protein from Staphylococcus aureus | ||||||
Components | Fibrinogen binding protein | ||||||
Keywords | PROTEIN BINDING / The fibrinogen binding protein / structural genomics / MCSG. / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information ibrinogen binding protein from staphylococcus aureus fold / ibrinogen binding protein from staphylococcus aureus domain / fibrinogen binding protein from staphylococcus aureus domain like / Ribonuclease HI; Chain A / Rqc2 homolog RqcH, bacterial / NFACT, RNA-binding domain / NFACT protein RNA binding domain / Helicase, Ruva Protein; domain 3 - #50 / Helicase, Ruva Protein; domain 3 / Roll ...ibrinogen binding protein from staphylococcus aureus fold / ibrinogen binding protein from staphylococcus aureus domain / fibrinogen binding protein from staphylococcus aureus domain like / Ribonuclease HI; Chain A / Rqc2 homolog RqcH, bacterial / NFACT, RNA-binding domain / NFACT protein RNA binding domain / Helicase, Ruva Protein; domain 3 - #50 / Helicase, Ruva Protein; domain 3 / Roll / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Staphylococcus aureus subsp. aureus Mu50 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.81 Å | ||||||
Authors | Zhang, R. / Wu, R. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published / Year: 2008 Title: The crystal structure of the fibrinogen binding protein from Staphylococcus aureus Authors: Zhang, R. / Wu, R. / Freeman, L. / Joachimiak, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3doa.cif.gz | 65.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3doa.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 3doa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3doa_validation.pdf.gz | 428.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3doa_full_validation.pdf.gz | 438.2 KB | Display | |
Data in XML | 3doa_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 3doa_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/3doa ftp://data.pdbj.org/pub/pdb/validation_reports/do/3doa | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | protein existed as monomer |
-Components
#1: Protein | Mass: 33611.199 Da / Num. of mol.: 1 / Fragment: residues 1-288 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria) Strain: ubsp. aureus Mu50 / Gene: SAV1208 / Plasmid: PDM68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q99UR0, UniProt: A0A0H3JV08*PLUS |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.11 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10% PEG4000, 45% tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2007 / Details: mirrors |
Radiation | Monochromator: Si channel 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→87.04 Å / Num. all: 10661 / Num. obs: 10541 / % possible obs: 98.87 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 16.9 % / Rsym value: 0.145 / Net I/σ(I): 21.84 |
Reflection shell | Resolution: 2.81→2.88 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.639 / % possible all: 88.09 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.81→87.04 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.891 / SU B: 29.329 / SU ML: 0.269 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.633 / ESU R Free: 0.357 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.353 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.81→87.04 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.808→2.88 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 46.629 Å / Origin y: 24.733 Å / Origin z: 73.341 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|