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Open data
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Basic information
Entry | Database: PDB / ID: 1pci | ||||||
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Title | PROCARICAIN | ||||||
![]() | PROCARICAIN | ||||||
![]() | THIOL PROTEASE / ZYMOGEN / HYDROLASE | ||||||
Function / homology | ![]() caricain / proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Groves, M.R. / Taylor, M.A.J. / Scott, M. / Cummings, N.J. / Pickersgill, R.W. / Jenkins, J.A. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 168.2 KB | Display | ![]() |
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PDB format | ![]() | 141.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ppoS S: Starting model for refinement |
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Similar structure data |
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Links
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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. |
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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.) ![]() ![]() ![]() ![]() Source details | PROCARICAI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() | |||||||||
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 % |
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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: ![]() | ||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 53.7 Å2 |