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Yorodumi- PDB-1stf: THE REFINED 2.4 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF RECOMBINANT ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1stf | ||||||
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Title | THE REFINED 2.4 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF RECOMBINANT HUMAN STEFIN B IN COMPLEX WITH THE CYSTEINE PROTEINASE PAPAIN: A NOVEL TYPE OF PROTEINASE INHIBITOR INTERACTION | ||||||
Components |
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Keywords | HYDROLASE(SULFHYDRYL PROTEINASE) | ||||||
Function / homology | Function and homology information papain / negative regulation of peptidase activity / cysteine-type endopeptidase inhibitor activity / endopeptidase inhibitor activity / serpin family protein binding / cysteine-type peptidase activity / adult locomotory behavior / negative regulation of proteolysis / tertiary granule lumen / collagen-containing extracellular matrix ...papain / negative regulation of peptidase activity / cysteine-type endopeptidase inhibitor activity / endopeptidase inhibitor activity / serpin family protein binding / cysteine-type peptidase activity / adult locomotory behavior / negative regulation of proteolysis / tertiary granule lumen / collagen-containing extracellular matrix / secretory granule lumen / protease binding / ficolin-1-rich granule lumen / Neutrophil degranulation / nucleolus / proteolysis / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Carica papaya (papaya) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.37 Å | ||||||
Authors | Stubbs, M.T. / Laber, B. / Bode, W. | ||||||
Citation | Journal: EMBO J. / Year: 1990 Title: The refined 2.4 A X-ray crystal structure of recombinant human stefin B in complex with the cysteine proteinase papain: a novel type of proteinase inhibitor interaction. Authors: Stubbs, M.T. / Laber, B. / Bode, W. / Huber, R. / Jerala, R. / Lenarcic, B. / Turk, V. #1: Journal: FEBS Lett. / Year: 1991 Title: Minireview: The Cystatins: Protein Inhibitors of Cysteine Proteinases Authors: Turk, V. / Bode, W. #2: Journal: Biol.Chem.Hoppe-Seyler / Year: 1990 Title: Mutations in the Qvvag Region of the Cysteine Proteinase Inhibitor Stefin B Authors: Jerala, R. / Trstenjak-Prebanda, M. / Kroon-Zitko, L. / Lenarcic, B. / Turk, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1stf.cif.gz | 70.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1stf.ent.gz | 56.4 KB | Display | PDB format |
PDBx/mmJSON format | 1stf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/st/1stf ftp://data.pdbj.org/pub/pdb/validation_reports/st/1stf | 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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Atom site foot note | 1: CIS PROLINE - PRO E 152 2: VAL I 66 - GLY I 67 OMEGA =214.83 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
-Components
#1: Protein | Mass: 23507.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Carica papaya (papaya) / Organ: FRUIT / Production host: Escherichia coli (E. coli) / References: UniProt: P00784, papain |
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#2: Protein | Mass: 11173.570 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Organ: FRUIT / Production host: Escherichia coli (E. coli) / References: UniProt: P04080 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.1 % | |||||||||||||||
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Crystal grow | *PLUS pH: 5 / Method: vapor diffusion, sitting drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.37 Å / Num. obs: 16084 / % possible obs: 89 % / Rmerge(I) obs: 0.102 |
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Reflection shell | *PLUS Highest resolution: 2.37 Å / Lowest resolution: 2.44 Å |
-Processing
Software | Name: EREF / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.37→8 Å /
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Refinement step | Cycle: LAST / Resolution: 2.37→8 Å
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Refine LS restraints |
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Software | *PLUS Name: EREF / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.37 Å / Lowest resolution: 8 Å / Num. reflection obs: 16033 / Rfactor obs: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: o_angle_d / Dev ideal: 2.1 |