+Open data
-Basic information
Entry | Database: PDB / ID: 200 | ||||||
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Title | Crystal structure of H369L mutant of yeast bleomycin hydrolase | ||||||
Components | Cysteine proteinase 1 | ||||||
Keywords | HYDROLASE / bleomycin hydrolase / thiol protease / C1 protease | ||||||
Function / homology | Function and homology information bleomycin hydrolase / cysteine-type aminopeptidase activity / homocysteine catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / aminopeptidase activity / cysteine-type peptidase activity / response to toxic substance / single-stranded DNA binding / double-stranded DNA binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...bleomycin hydrolase / cysteine-type aminopeptidase activity / homocysteine catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / aminopeptidase activity / cysteine-type peptidase activity / response to toxic substance / single-stranded DNA binding / double-stranded DNA binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cysteine-type endopeptidase activity / response to antibiotic / mRNA binding / negative regulation of transcription by RNA polymerase II / mitochondrion / proteolysis / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / isomorphous replacement / Resolution: 2.2 Å | ||||||
Authors | O'Farrell, P.A. / Joshua-Tor, L. | ||||||
Citation | Journal: Biochem.J. / Year: 2007 Title: Mutagenesis and crystallographic studies of the catalytic residues of the papain family protease bleomycin hydrolase: new insights into active-site structure Authors: O'Farrell, P.A. / Joshua-Tor, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e02.cif.gz | 103.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e02.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 2e02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/2e02 ftp://data.pdbj.org/pub/pdb/validation_reports/e0/2e02 | HTTPS FTP |
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-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: 52401.668 Da / Num. of mol.: 1 / Mutation: H369L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Escherichia coli (E. coli) / References: UniProt: Q01532, bleomycin hydrolase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.86 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 14-20% PEG 4K, 100mM Tris-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 27215 / Biso Wilson estimate: 14.1 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: isomorphous replacement / Resolution: 2.2→49.94 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 606883.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.0489 Å2 / ksol: 0.335612 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→49.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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