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Yorodumi- PDB-2qaa: Crystal structure of the second tetrahedral intermediates of SGPB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qaa | ||||||
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Title | Crystal structure of the second tetrahedral intermediates of SGPB at pH 7.3 | ||||||
Components | Streptogrisin-B | ||||||
Keywords | HYDROLASE / CHYMOTRYPSIN-TYPE SERINE PEPTIDASE / SECOND TETRAHEDRAL INTERMEDIATES / SINGLE AMINO ACIDS / BETA BARRELS / ALPHA HELIX | ||||||
Function / homology | Function and homology information streptogrisin B / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Streptomyces griseus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.23 Å | ||||||
Authors | Lee, T.W. / James, M.N.G. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2008 Title: 1.2A-resolution crystal structures reveal the second tetrahedral intermediates of streptogrisin B (SGPB). Authors: Lee, T.W. / James, M.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qaa.cif.gz | 175.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qaa.ent.gz | 145.7 KB | Display | PDB format |
PDBx/mmJSON format | 2qaa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/2qaa ftp://data.pdbj.org/pub/pdb/validation_reports/qa/2qaa | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | Each asymmetric unit contains two SGPB molecules. SGPB functions as a monomer. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 18653.232 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Streptomyces griseus (bacteria) / References: UniProt: P00777, streptogrisin B |
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-Non-polymers , 9 types, 552 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-EPE / | #8: Chemical | ChemComp-GOL / #9: Chemical | #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 10 mg/mL SGPB in 10 mM MgCl2 1.0 M Li2SO4, 0.1 M HEPES-NaOH pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.127 Å |
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 22, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 1.23→40 Å / Num. obs: 136369 / % possible obs: 99 % / Redundancy: 8.5 % / Rsym value: 0.048 / Net I/σ(I): 37.3 |
Reflection shell | Resolution: 1.23→1.27 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3 / Rsym value: 0.404 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Resolution: 1.23→40 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.979 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.23→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.23→1.262 Å / Total num. of bins used: 20
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