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Yorodumi- PDB-3l1k: SAD structure solution of proteinase K grown in potassium tellura... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l1k | ||||||
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Title | SAD structure solution of proteinase K grown in potassium tellurate solution | ||||||
Components | Proteinase K | ||||||
Keywords | HYDROLASE / ortho- meta- tellurate / Metal-binding / Serine protease / Zymogen | ||||||
Function / homology | Function and homology information peptidase K / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Tritirachium album (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.55 Å | ||||||
Authors | Jakoncic, J. | ||||||
Citation | Journal: To be Published Title: SAD structure solution of proteinase K grown in potassium tellurate solution Authors: Jakoncic, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l1k.cif.gz | 127.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l1k.ent.gz | 104.4 KB | Display | PDB format |
PDBx/mmJSON format | 3l1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/3l1k ftp://data.pdbj.org/pub/pdb/validation_reports/l1/3l1k | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28958.791 Da / Num. of mol.: 1 / Fragment: residues 106-384 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tritirachium album (fungus) / Gene: PROK / References: UniProt: P06873, peptidase K |
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-Non-polymers , 5 types, 429 molecules
#2: Chemical | ChemComp-CA / | ||||
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#3: Chemical | ChemComp-TE6 / | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | RESIDUE 207 IS UNAMBIGUOUSLY IDENTIFIED AS ASP FROM THE ELECTRON DENSITY MAP EVEN THOUGH THE ...RESIDUE 207 IS UNAMBIGUOU |
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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: 2.03 Å3/Da / Density % sol: 39.52 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Drop was 1 microL of protein solution (80 mg/mL in dH2O) and 1 microL of well solution (1 mL of saturated solution of K2TeO4. The cryo-solution consisted of 70% of the crystallization ...Details: Drop was 1 microL of protein solution (80 mg/mL in dH2O) and 1 microL of well solution (1 mL of saturated solution of K2TeO4. The cryo-solution consisted of 70% of the crystallization solution and 30% of ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.2398 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 14, 2007 / Details: Rh coated toroidal focusing mirror. |
Radiation | Monochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2398 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→30 Å / Num. all: 340169 / % possible obs: 95.1 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 40 |
Reflection shell | Resolution: 1.55→1.61 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 9.7 / Num. unique all: 9880 / % possible all: 67.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.55→30 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.92 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.527 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Total num. of bins used: 20
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