+Open data
-Basic information
Entry | Database: PDB / ID: 1cb5 | ||||||
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Title | HUMAN BLEOMYCIN HYDROLASE. | ||||||
Components | BLEOMYCIN HYDROLASE | ||||||
Keywords | HYDROLASE / AMINOPEPTIDASE / CYSTEINE PROTEASE / SELF-COMPARTMENTALIZING / BLEOMYCIN | ||||||
Function / homology | Function and homology information bleomycin hydrolase / cysteine-type aminopeptidase activity / homocysteine catabolic process / aminopeptidase activity / cysteine-type peptidase activity / carboxypeptidase activity / response to toxic substance / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / response to xenobiotic stimulus ...bleomycin hydrolase / cysteine-type aminopeptidase activity / homocysteine catabolic process / aminopeptidase activity / cysteine-type peptidase activity / carboxypeptidase activity / response to toxic substance / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / response to xenobiotic stimulus / cysteine-type endopeptidase activity / proteolysis / extracellular exosome / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | O'Farrell, P.A. / Gonzalez, F. / Zheng, W. / Johnston, S.A. / Joshua-Tor, L. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: Crystal structure of human bleomycin hydrolase, a self-compartmentalizing cysteine protease. Authors: O'Farrell, P.A. / Gonzalez, F. / Zheng, W. / Johnston, S.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 | 1cb5.cif.gz | 270.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cb5.ent.gz | 222.2 KB | Display | PDB format |
PDBx/mmJSON format | 1cb5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cb5_validation.pdf.gz | 382.3 KB | Display | wwPDB validaton report |
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Full document | 1cb5_full_validation.pdf.gz | 401.4 KB | Display | |
Data in XML | 1cb5_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 1cb5_validation.cif.gz | 42.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/1cb5 ftp://data.pdbj.org/pub/pdb/validation_reports/cb/1cb5 | HTTPS FTP |
-Related structure data
Related structure data | 2cb5C 1gcbS S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 52342.754 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Plasmid: PKH260HUBH / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/PLYSS References: UniProt: Q13867, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.59 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.00 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 8 / 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: NSLS / Beamline: X26C / Wavelength: 1.126 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.126 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→100 Å / Num. obs: 47154 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 39.1 Å2 / Rsym value: 7.2 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.59→2.68 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 43.1 / % possible all: 94 |
Reflection | *PLUS Highest resolution: 2.59 Å / Lowest resolution: 25 Å / % possible obs: 91.6 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Num. measured all: 242494 / Rmerge(I) obs: 0.072 / Biso Wilson estimate: 39.1 Å2 |
Reflection shell | *PLUS Highest resolution: 2.59 Å / Lowest resolution: 2.68 Å / % possible obs: 94 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 3.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GCB Resolution: 2.59→100 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 274249.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT Details: RESIDUES 384-387 LIE IN A LOOP REGION FOR WHICH THE DENSITY IS DIFFICULT TO INTERPRET. THEY HAVE BEEN MODELED, BUT OCCUPANCY HAS BEEN SET TO ZERO FOR NON-MAINCHAIN ATOMS. OCCUPANCY HAS ALSO ...Details: RESIDUES 384-387 LIE IN A LOOP REGION FOR WHICH THE DENSITY IS DIFFICULT TO INTERPRET. THEY HAVE BEEN MODELED, BUT OCCUPANCY HAS BEEN SET TO ZERO FOR NON-MAINCHAIN ATOMS. OCCUPANCY HAS ALSO BEEN SET TO ZERO FOR SOME SIDE-CHAIN ATOMS ON THE PROTEIN SURFACE.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 23.49 Å2 / ksol: 0.322 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.59→100 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.59→2.75 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.59 Å / Lowest resolution: 25 Å / Rfactor obs: 0.238 / Rfactor Rfree: 0.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.323 / Rfactor Rwork: 0.303 / Rfactor obs: 0.304 |