+Open data
-Basic information
Entry | Database: PDB / ID: 1pci | ||||||
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Title | PROCARICAIN | ||||||
Components | PROCARICAIN | ||||||
Keywords | THIOL PROTEASE / ZYMOGEN / HYDROLASE | ||||||
Function / homology | Function and homology information caricain / proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space Similarity search - Function | ||||||
Biological species | Carica papaya (papaya) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / COMBINED MOLECULAR REPLACEMENT, ISOMORPHOUS REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Groves, M.R. / Taylor, M.A.J. / Scott, M. / Cummings, N.J. / Pickersgill, R.W. / Jenkins, J.A. | ||||||
Citation | Journal: Structure / Year: 1996 Title: The prosequence of procaricain forms an alpha-helical domain that prevents access to the substrate-binding cleft. Authors: Groves, M.R. / Taylor, M.A. / Scott, M. / Cummings, N.J. / Pickersgill, R.W. / Jenkins, J.A. #1: Journal: Acta Crystallogr.,Sect.B / Year: 1991 Title: Determination of the Structure of Papaya Protease Omega Authors: Pickersgill, R.W. / Rizkallah, P. / Harris, G.W. / Goodenough, P.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pci.cif.gz | 168.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pci.ent.gz | 141.2 KB | Display | PDB format |
PDBx/mmJSON format | 1pci.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pci_validation.pdf.gz | 419.7 KB | Display | wwPDB validaton report |
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Full document | 1pci_full_validation.pdf.gz | 450.3 KB | Display | |
Data in XML | 1pci_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 1pci_validation.cif.gz | 29.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pc/1pci ftp://data.pdbj.org/pub/pdb/validation_reports/pc/1pci | HTTPS FTP |
-Related structure data
Related structure data | 1ppoS 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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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE DEPOSITOR PROVIDED COORDINATES FOR CHAIN A. THE OTHER TWO CHAINS IN THE ASYMMETRIC UNIT WERE GENERATED BY THE PROTEIN DATA BANK USING THE MTRIX TRANSFORMATIONS BELOW. |
-Components
#1: Protein | Mass: 35940.328 Da / Num. of mol.: 3 / Mutation: H159G Source method: isolated from a genetically manipulated source Details: ACTIVE SITE HIS MUTATION / Source: (gene. exp.) Carica papaya (papaya) / Tissue: LEAF / Gene: OMEGA / Plasmid: PET3A / Gene (production host): OMEGA / Production host: Escherichia coli (E. coli) / References: UniProt: P10056, chymopapain Source details | PROCARICAI | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 3.84 Å3/Da / Density % sol: 62 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7. | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 11 ℃ / pH: 5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87, 1.0 | |||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 23, 1994 | |||||||||
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 3.2→96.2 Å / Num. obs: 27079 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Biso Wilson estimate: 0.29 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 3.8 | |||||||||
Reflection shell | Resolution: 3.21→3.34 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.169 / % possible all: 98.6 | |||||||||
Reflection shell | *PLUS % possible obs: 98.6 % |
-Processing
Software |
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Refinement | Method to determine structure: COMBINED MOLECULAR REPLACEMENT, ISOMORPHOUS REPLACEMENT Starting model: MATURE CARICAIN (PDB ENTRY 1PPO) Resolution: 3.2→90.6 Å / Rfactor Rfree error: 0.0075 / Cross valid method: FREE R / σ(F): 1 Details: ELECTRON DENSITY FOR THE POLYPEPTIDE CHAIN 90P - 103P IS POOR. THE STRUCTURE WAS PRIMARILY MODELED IN THIS REGION. NCS RESTRAINTS WERE RELAXED FOR THE POLYPEPTIDE CHAIN 88P - 100P DUE TO NCS PACKING CLASHES.
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Displacement parameters | Biso mean: 0.94 Å2
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Refine analyze | Luzzati d res low obs: 96.2 Å | ||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→90.6 Å
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Refine LS restraints NCS | Weight Biso : 1 / Weight position: 300 | ||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.22 Å / Rfactor Rfree error: 0.0072
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TPOH19.PEP | ||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 53.7 Å2 |