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Yorodumi- PDB-5fnw: Crystal structure at pH 7.0 of a potato STI-Kunitz bi-functional ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fnw | ||||||
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Title | Crystal structure at pH 7.0 of a potato STI-Kunitz bi-functional inhibitor of serine and aspartic proteases in space group p4322 and ph 9.0 | ||||||
Components | POTATO STI-KUNITZ BI-FUNCTIONAL INHIBITOR E3AD_N19D | ||||||
Keywords | HYDROLASE INHIBITOR / HYDROLASE / STI-KUNITZ INHIBITOR / ASPARTIC PROTEASES / SERINE PROTEASES / PROTEASE INHIBITOR / BI-FUNCTIONAL PROTEASE INHIBITOR / KUNITZ-TYPE INHIBITOR | ||||||
Function / homology | Function and homology information serine-type endopeptidase inhibitor activity / peptidase activity / proteolysis Similarity search - Function | ||||||
Biological species | SOLANUM TUBEROSUM (potato) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Guerra, Y. / Rudino-Pinera, E. | ||||||
Citation | Journal: J. Struct. Biol. / Year: 2016 Title: Structures of a bi-functional Kunitz-type STI family inhibitor of serine and aspartic proteases: Could the aspartic protease inhibition have evolved from a canonical serine protease-binding loop? Authors: Guerra, Y. / Valiente, P.A. / Pons, T. / Berry, C. / Rudino-Pinera, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fnw.cif.gz | 48 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fnw.ent.gz | 34.8 KB | Display | PDB format |
PDBx/mmJSON format | 5fnw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fnw_validation.pdf.gz | 421.4 KB | Display | wwPDB validaton report |
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Full document | 5fnw_full_validation.pdf.gz | 424.8 KB | Display | |
Data in XML | 5fnw_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 5fnw_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/5fnw ftp://data.pdbj.org/pub/pdb/validation_reports/fn/5fnw | HTTPS FTP |
-Related structure data
Related structure data | 5fnxC 5fzuC 5fzyC 5fzzC 5g00C 3tc2S C: citing same article (ref.) 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
#1: Protein | Mass: 20527.557 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THE SEQUENCE OF THE POTATO STI-KUNITZ BI- FUNCTIONAL INHIBITOR E3AD_N19D HAS NOT BEEN DEPOSITED AT UNIPROT NOR GENBANK. MUTANT N19D Source: (gene. exp.) SOLANUM TUBEROSUM (potato) / Variant: ESTIMA / Plasmid: PPICZALPHAC / Production host: KOMAGATAELLA PASTORIS GS115 (fungus) / References: UniProt: M1AKE5*PLUS |
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#2: Water | ChemComp-HOH / |
Sequence details | WHEN POTATO STI-KUNITZ BI-FUNCTIONAL INHIBITOR E3AD_N19D WAS SEQUENCED RESIDUES 19 AND 177 WERE N ...WHEN POTATO STI-KUNITZ BI-FUNCTIONAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.09 % / Description: NONE |
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Crystal grow | pH: 7 Details: CRYSTAL WAS CRYSTALLIZED FROM 15% (W/V) PEG 20000, 0.1 M HEPES PH 7.0, 30 MM GLYCYL-GLYCYL-GLYCINE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 24, 2015 / Details: MICROBEAM |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→19.5 Å / Num. obs: 10963 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 18.5 % / Biso Wilson estimate: 58.19 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 38.01 |
Reflection shell | Resolution: 2.45→2.5 Å / Redundancy: 19.28 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 5.58 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3TC2 Resolution: 2.45→19.497 Å / SU ML: 0.43 / σ(F): 1.37 / Phase error: 29.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→19.497 Å
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Refine LS restraints |
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LS refinement shell |
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