+Open data
-Basic information
Entry | Database: PDB / ID: 7v5s | ||||||
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Title | Crystal structure of human bleomycin hydrolase C73A mutant | ||||||
Components | Bleomycin hydrolase | ||||||
Keywords | HYDROLASE / cysteine protease | ||||||
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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å | ||||||
Authors | Chang, C.Y. / Zheng, Y.Z. / Huang, S.J. / Wang, Y.L. / Toh, S.I. / Lin, E.C. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Chembiochem / Year: 2022 Title: The Structure-Function Relationship of Human Bleomycin Hydrolase: Mutation of a Cysteine Protease into a Serine Protease. Authors: Zheng, Y.Z. / Cui, J. / Wang, Y.L. / Huang, S.J. / Lin, E.C. / Huang, S.C. / Rudolf, J.D. / Yan, X. / Chang, C.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v5s.cif.gz | 108.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v5s.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 7v5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7v5s_validation.pdf.gz | 856.1 KB | Display | wwPDB validaton report |
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Full document | 7v5s_full_validation.pdf.gz | 861.1 KB | Display | |
Data in XML | 7v5s_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 7v5s_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/7v5s ftp://data.pdbj.org/pub/pdb/validation_reports/v5/7v5s | HTTPS FTP |
-Related structure data
Related structure data | 7v5lSC 7v5tC 7xf9C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54767.387 Da / Num. of mol.: 1 / Mutation: C73A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BLMH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13867, bleomycin hydrolase |
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#2: Chemical | ChemComp-PG4 / |
#3: Chemical | ChemComp-PGE / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 12.26 Å3/Da / Density % sol: 89.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30% (w/v) PEG 400, 0.1mM CHES, pH 9.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.9732 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9732 Å / Relative weight: 1 |
Reflection | Resolution: 3.02→30 Å / Num. obs: 53491 / % possible obs: 100 % / Redundancy: 11.3 % / CC1/2: 0.98 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 3.02→3.13 Å / Redundancy: 11.9 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5272 / CC1/2: 0.865 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7V5L Resolution: 3.02→29.83 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.095 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 144.08 Å2 / Biso mean: 63.93 Å2 / Biso min: 39.38 Å2
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Refinement step | Cycle: final / Resolution: 3.02→29.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.023→3.101 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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