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Yorodumi- PDB-3beu: Na+-Dependent Allostery Mediates Coagulation Factor Protease Acti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3beu | ||||||
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Title | Na+-Dependent Allostery Mediates Coagulation Factor Protease Active Site Selectivity | ||||||
Components | Trypsin | ||||||
Keywords | HYDROLASE / beta sheets / serine protease / Zymogen | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces griseus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å | ||||||
Authors | Page, M.J. / Carrell, C.J. / Di Cera, E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Engineering protein allostery: 1.05 A resolution structure and enzymatic properties of a Na+-activated trypsin. Authors: Page, M.J. / Carrell, C.J. / Di Cera, E. | ||||||
History |
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Remark 999 | The insertions T98, Y99 and the deletion P185 were introduced by mutagenesis |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3beu.cif.gz | 211.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3beu.ent.gz | 166.2 KB | Display | PDB format |
PDBx/mmJSON format | 3beu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/be/3beu ftp://data.pdbj.org/pub/pdb/validation_reports/be/3beu | HTTPS FTP |
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-Related structure data
Related structure data | 1os8S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23539.453 Da / Num. of mol.: 2 Mutation: Y94F, N95T,G96K, T97E, A171S, Y172S, G173S, N174F, E175I, E180M, G186K,G187Q, V188E, I208V, Y217E, P222K, Y224K, P225Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces griseus (bacteria) / Gene: sprT / Production host: Bacillus subtilis (bacteria) / References: UniProt: P00775, trypsin |
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-Non-polymers , 5 types, 624 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-BEN / #4: Chemical | #5: Chemical | #6: 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: 1.97 Å3/Da / Density % sol: 37.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1.6 M ammonium sulfate, 10 mM calcium acetate, 50 mM sodium chloride, 10 mM benzamidine, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2007 |
Radiation | Monochromator: Ge (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9002 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→50 Å / Num. all: 173357 / Num. obs: 173357 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 1.05→1.07 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.384 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OS8 Resolution: 1.05→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.05→10 Å
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Refine LS restraints |
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