[English] 日本語
Yorodumi- PDB-1meg: CRYSTAL STRUCTURE OF A CARICAIN D158E MUTANT IN COMPLEX WITH E-64 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1meg | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF A CARICAIN D158E MUTANT IN COMPLEX WITH E-64 | ||||||
Components | CARICAIN | ||||||
Keywords | HYDROLASE / CYSTEINE PROTEINASE / THIOL PROTEASE | ||||||
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 / Resolution: 2 Å | ||||||
Authors | Katerelos, N.A. | ||||||
Citation | Journal: FEBS Lett. / Year: 1996 Title: Crystal structure of a caricain D158E mutant in complex with E-64. Authors: Katerelos, N.A. / Taylor, M.A. / Scott, M. / Goodenough, P.W. / Pickersgill, R.W. #1: Journal: To be Published Title: Rapid Kinetics Studies and Structural Determination of a Cysteine Proteinase Mutant Implies that Residue Asp 158 in Caricain Has a Major Effect Upon the Ability of the Active Site Histidine to ...Title: Rapid Kinetics Studies and Structural Determination of a Cysteine Proteinase Mutant Implies that Residue Asp 158 in Caricain Has a Major Effect Upon the Ability of the Active Site Histidine to Protonate a Dipyridyl Probe Authors: Katerelos, A. / Goodenough, P.W. #2: Journal: Protein Eng. / Year: 1994 Title: An Unequivocal Example of Cysteine Proteinase Activity Affected by Multiple Electrostatic Interactions Authors: Taylor, M.A. / Baker, K.C. / Connerton, I.F. / Cummings, N.J. / Harris, G.W. / Henderson, I.M. / Jones, S.T. / Pickersgill, R.W. / Sumner, I.G. / Warwicker, J. / al., et #3: Journal: Gene / Year: 1993 Title: Nucleotide Sequence and Expression in Escherichia Coli of Cdnas Encoding Papaya Proteinase Omega from Carica Papaya Authors: Revell, D.F. / Cummings, N.J. / Baker, K.C. / Collins, M.E. / Taylor, M.A. / Sumner, I.G. / Pickersgill, R.W. / Connerton, I.F. / Goodenough, P.W. #4: Journal: Protein Eng. / Year: 1992 Title: Active Papain Renatured and Processed from Insoluble Recombinant Propapain Expressed in Escherichia Coli Authors: Taylor, M.A. / Pratt, K.A. / Revell, D.F. / Baker, K.C. / Sumner, I.G. / Goodenough, P.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1meg.cif.gz | 52.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1meg.ent.gz | 40.1 KB | Display | PDB format |
PDBx/mmJSON format | 1meg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1meg_validation.pdf.gz | 645.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1meg_full_validation.pdf.gz | 648.7 KB | Display | |
Data in XML | 1meg_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 1meg_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/1meg ftp://data.pdbj.org/pub/pdb/validation_reports/me/1meg | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23339.770 Da / Num. of mol.: 1 / Mutation: D158E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Carica papaya (papaya) / Plasmid: PLYSS / Production host: Escherichia coli (E. coli) / Strain (production host): PET / References: UniProt: P10056, caricain |
---|---|
#2: Chemical | ChemComp-E64 / |
#3: Chemical | ChemComp-EOH / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 34.2 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
---|---|
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Nov 10, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Num. obs: 12010 / % possible obs: 86 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.06 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 7.72 Å / % possible obs: 86 % / Num. measured all: 42446 / Rmerge(I) obs: 0.06 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2→10 Å / σ(F): 2 Details: ATOMS C13, C14, C15, N3, C16, N4 AND N5 OF E64 WERE NOT VISIBLE IN DENSITY BECAUSE OF THE HIGH MOBILITY OF THAT PART OF THE E-64 MOLECULE WHICH ACCOUNTS FOR THEIR HIGH TEMPERATURE FACTORS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|