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Yorodumi- PDB-2pbh: CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN B AT 3.3 ANGSTROM RESOLUTION -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pbh | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN PROCATHEPSIN B AT 3.3 ANGSTROM RESOLUTION | ||||||
Components | PROCATHEPSIN B | ||||||
Keywords | THIOL PROTEASE / CATHEPSIN B / CYSTEINE PROTEASE / PROENZYME / PAPAIN | ||||||
Function / homology | Function and homology information cathepsin B / peptidase inhibitor complex / thyroid hormone generation / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / decidualization ...cathepsin B / peptidase inhibitor complex / thyroid hormone generation / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / decidualization / collagen catabolic process / cysteine-type peptidase activity / epithelial cell differentiation / collagen binding / MHC class II antigen presentation / proteolysis involved in protein catabolic process / melanosome / peptidase activity / regulation of apoptotic process / collagen-containing extracellular matrix / ficolin-1-rich granule lumen / lysosome / symbiont entry into host cell / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / Neutrophil degranulation / perinuclear region of cytoplasm / proteolysis / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Podobnik, M. / Turk, D. / Kuhelj, R. / Turk, V. | ||||||
Citation | Journal: FEBS Lett. / Year: 1996 Title: Crystal structures of human procathepsin B at 3.2 and 3.3 Angstroms resolution reveal an interaction motif between a papain-like cysteine protease and its propeptide. Authors: Turk, D. / Podobnik, M. / Kuhelj, R. / Dolinar, M. / Turk, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pbh.cif.gz | 77.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pbh.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 2pbh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pbh_validation.pdf.gz | 367.8 KB | Display | wwPDB validaton report |
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Full document | 2pbh_full_validation.pdf.gz | 380 KB | Display | |
Data in XML | 2pbh_validation.xml.gz | 9 KB | Display | |
Data in CIF | 2pbh_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/2pbh ftp://data.pdbj.org/pub/pdb/validation_reports/pb/2pbh | HTTPS FTP |
-Related 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: 35226.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P07858, cathepsin B |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 48 % | |||||||||||||||
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Crystal grow | pH: 7.2 Details: PROTEIN WAS CRYSTALLIZED FROM 2 M AMMONIUM SULFATE, 700 MM TRIS, PH 7.2 | |||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.1 / Method: vapor diffusion, sitting drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1995 / Details: COLLIMATOR |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→8 Å / Num. obs: 4297 / % possible obs: 94.2 % / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Rmerge(I) obs: 0.186 / Rsym value: 0.08 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 3.3→3.4 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.066 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.316 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY Resolution: 3.3→10 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 3.3→10 Å
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Software | *PLUS Name: MAIN / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Num. reflection all: 4297 / Rfactor Rfree: 0.269 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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