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Yorodumi- PDB-1s2n: Crystal structure of a cold adapted subtilisin-like serine proteinase -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s2n | ||||||
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Title | Crystal structure of a cold adapted subtilisin-like serine proteinase | ||||||
Components | extracellular subtilisin-like serine proteinase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Vibrio sp. PA-44 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.44 Å | ||||||
Authors | Arnorsdottir, J. / Kristjansson, M.M. / Ficner, R. | ||||||
Citation | Journal: FEBS J. / Year: 2005 Title: Crystal structure of a subtilisin-like serine proteinase from a psychrotrophic Vibrio species reveals structural aspects of cold adaptation. Authors: Arnorsdottir, J. / Kristjansson, M.M. / Ficner, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s2n.cif.gz | 123 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s2n.ent.gz | 92.9 KB | Display | PDB format |
PDBx/mmJSON format | 1s2n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1s2n_validation.pdf.gz | 457 KB | Display | wwPDB validaton report |
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Full document | 1s2n_full_validation.pdf.gz | 465.5 KB | Display | |
Data in XML | 1s2n_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 1s2n_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/1s2n ftp://data.pdbj.org/pub/pdb/validation_reports/s2/1s2n | HTTPS FTP |
-Related structure data
Related structure data | 1sh7C 1ic6S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 1 / Auth seq-ID: 3 - 273 / Label seq-ID: 3 - 273
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-Components
#1: Protein | Mass: 29002.395 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio sp. PA-44 (bacteria) / Plasmid: pBAD TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 References: UniProt: Q8GB52, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Chemical | ChemComp-CA / #3: Chemical | #4: 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: 2.01 Å3/Da / Density % sol: 38.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8 Details: PEG 4000, isopropanol, HEPES, pH 8.0, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 10, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→30 Å / Num. all: 17252 / Num. obs: 17252 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rsym value: 0.141 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.44→2.53 Å / Mean I/σ(I) obs: 3.4 / Num. unique all: 1617 / Rsym value: 0.43 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Homology model based on PDB entry 1IC6 Resolution: 2.44→29.11 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.892 / SU B: 10.066 / SU ML: 0.228 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.336 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.227 Å2
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Refinement step | Cycle: LAST / Resolution: 2.44→29.11 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1907 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.44→2.503 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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