+Open data
-Basic information
Entry | Database: PDB / ID: 1qqr | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF STREPTOKINASE DOMAIN B | ||||||
Components | STREPTOKINASE DOMAIN B | ||||||
Keywords | HYDROLASE ACTIVATOR / NON-PROTEOLYTIC / PLASMINOGEN ACTIVATION / FIBRINOLYSIS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus dysgalactiae subsp. equisimilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Spraggon, G. / Zhang, X.X. / Ponting, C.P. / Fox, V.F. / Phillips, C. / Smith, R.A.G. / Jones, E.Y. / Dobson, C. / Stuart, D.I. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Streptokinse Domain B Authors: Spraggon, G. / Zhang, X.X. / Ponting, C.P. / Fox, V.F. / Phillips, C. / Smith, R.A.G. / Jones, E.Y. / Dobson, C. / Stuart, D.I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1qqr.cif.gz | 127.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1qqr.ent.gz | 101.1 KB | Display | PDB format |
PDBx/mmJSON format | 1qqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qqr_validation.pdf.gz | 455.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1qqr_full_validation.pdf.gz | 479.1 KB | Display | |
Data in XML | 1qqr_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 1qqr_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/1qqr ftp://data.pdbj.org/pub/pdb/validation_reports/qq/1qqr | HTTPS FTP |
-Related structure data
Related structure data | 1bmlS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
3 |
| ||||||||||
4 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16021.934 Da / Num. of mol.: 4 / Fragment: B-DOMAIN / Source method: isolated from a natural source Source: (natural) Streptococcus dysgalactiae subsp. equisimilis (bacteria) Species: Streptococcus dysgalactiae / Strain: subsp. equisimilis / References: UniProt: P00779 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.63 % |
---|
-Data collection
Diffraction | Mean temperature: 150 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 34029 / Num. obs: 31237 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 44.7 Å2 / Rmerge(I) obs: 0.078 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BML Resolution: 2.3→50 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: MAXIMUM LIKELIHOOD REFINEMENT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 68.098 Å2 / ksol: 0.35326 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP |