+Open data
-Basic information
Entry | Database: PDB / ID: 2000 | ||||||
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Title | Crystal structure of NQ67E mutant of yeast bleomycin hydrolase | ||||||
Components | Cysteine proteinase 1 | ||||||
Keywords | HYDROLASE / bleomycin hydrolase / thiol protease / C1 proteas | ||||||
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: 2.13 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 | 2e03.cif.gz | 106.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e03.ent.gz | 81.2 KB | Display | PDB format |
PDBx/mmJSON format | 2e03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2e03_validation.pdf.gz | 428 KB | Display | wwPDB validaton report |
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Full document | 2e03_full_validation.pdf.gz | 435.6 KB | Display | |
Data in XML | 2e03_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 2e03_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/2e03 ftp://data.pdbj.org/pub/pdb/validation_reports/e0/2e03 | HTTPS FTP |
-Related structure data
Related structure data | 2dzyC 2dzzC 2e00C 2e01C 2e02C 1gcbS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 52427.641 Da / Num. of mol.: 1 / Mutation: Q67E 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: 56.82 % |
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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: 2.13→50 Å / Num. obs: 34254 / Biso Wilson estimate: 17.9 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: isomorphous replacement Starting model: 1gcb Resolution: 2.13→42.27 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 253082.78 / 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: 54.912 Å2 / ksol: 0.346772 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.13→42.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.13→2.26 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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