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Yorodumi- PDB-5g00: CRYSTAL STRUCTURE OF A POTATO STI-KUNITZ BIFUNCTIONAL INHIBITOR O... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g00 | ||||||
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Title | CRYSTAL STRUCTURE OF A POTATO STI-KUNITZ BIFUNCTIONAL INHIBITOR OF SERINE AND ASPARTIC PROTEASES IN SPACE GROUP P4322 AND PH 7.4 | ||||||
Components | KTI-A PROTEIN | ||||||
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: 2.5 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 | 5g00.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g00.ent.gz | 34.7 KB | Display | PDB format |
PDBx/mmJSON format | 5g00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/5g00 ftp://data.pdbj.org/pub/pdb/validation_reports/g0/5g00 | HTTPS FTP |
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-Related structure data
Related structure data | 5fnwSC 5fnxC 5fzuC 5fzyC 5fzzC 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: 20526.504 Da / Num. of mol.: 1 / Fragment: HYDROLASE INHIBITOR Source method: isolated from a genetically manipulated source Source: (gene. exp.) SOLANUM TUBEROSUM (potato) / Variant: ESTIMA / Plasmid: PPICZALPHAC / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): GS115 / References: UniProt: A0A097H118, UniProt: M1AKE5*PLUS |
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#2: Sugar | ChemComp-NAG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.52 % Description: DATA WAS ANISOTROPICALLY CORRECTED WITH THE WEBSERVER DIFFRACTION ANISOTROPY SERVER UCLA |
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Crystal grow | pH: 7.4 Details: 10% (W/V) PEG 2000 MME, 0.1 M TRIS-HCL PH 8.5, 0.2 M TRIMETHYLAMINE N-OXIDE, 30 MM GLYCYL-GLYCL-GLYCINE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.1807 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 17, 2016 / Details: SI (111) DOUBLE CRYSTAL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1807 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.5 Å / Num. obs: 10356 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 16.2 % / Biso Wilson estimate: 60.16 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 33.82 |
Reflection shell | Resolution: 2.5→2.57 Å / Redundancy: 16.63 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 4.89 / % possible all: 74.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5FNW Resolution: 2.5→36.021 Å / SU ML: 0.27 / σ(F): 1.37 / Phase error: 27.45 / 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 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.4 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→36.021 Å
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Refine LS restraints |
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LS refinement shell |
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