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Yorodumi- PDB-5om8: Crystal form 2 of Alpha1-antichymotrypsin variant DBS-II-allo: an... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5om8 | ||||||
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Title | Crystal form 2 of Alpha1-antichymotrypsin variant DBS-II-allo: an allosterically modulated drug-binding serpin for doxorubicin | ||||||
Components | (Alpha-1-antichymotrypsinAlpha 1-antichymotrypsin) x 2 | ||||||
Keywords | TRANSPORT PROTEIN / Serpin / alpha1-Antichymotrypsin / Doxorubicin-binding protein / allosterically triggered drug release | ||||||
Function / homology | Function and homology information maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / secretory granule lumen / collagen-containing extracellular matrix / blood microparticle ...maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / secretory granule lumen / collagen-containing extracellular matrix / blood microparticle / inflammatory response / Neutrophil degranulation / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Schmidt, K. / Muller, Y.A. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Design of an allosterically modulated doxycycline and doxorubicin drug-binding protein. Authors: Schmidt, K. / Gardill, B.R. / Kern, A. / Kirchweger, P. / Borsch, M. / Muller, Y.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5om8.cif.gz | 92.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5om8.ent.gz | 68 KB | Display | PDB format |
PDBx/mmJSON format | 5om8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/5om8 ftp://data.pdbj.org/pub/pdb/validation_reports/om/5om8 | HTTPS FTP |
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-Related structure data
Related structure data | 5om2C 5om3C 5om5C 5om6C 5om7C 6ftpC 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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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 41986.516 Da / Num. of mol.: 1 Mutation: L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F D278E A349R V355L K356E I357V T358L L359F L360Q S361G A362P P382D T383N D384F Q386W N387S Source method: isolated from a genetically manipulated source Details: all residues that are present in the sample sequence but not in the PDB file could not be modelled due to missing electron density Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA3, AACT, GIG24, GIG25 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: P01011 |
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#2: Protein/peptide | Mass: 4720.580 Da / Num. of mol.: 1 Mutation: L24R W194F W215Y E242Q K244N L269S P270Q K274S W276F R277F D278E A349R V355L K356E I357V T358L L359F L360Q S361G A362P P382D T383N D384F Q386W N387S Source method: isolated from a genetically manipulated source Details: all residues that are present in the sample sequence but not in the PDB file could not be modelled due to missing electron density Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINA3, AACT, GIG24, GIG25 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: P01011 |
-Non-polymers , 4 types, 151 molecules
#3: Chemical | ChemComp-CL / |
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#4: Chemical | ChemComp-EDO / |
#5: Chemical | ChemComp-NI / |
#6: 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: 2.15 Å3/Da / Density % sol: 42.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium chloride, 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40.6 Å / Num. obs: 20967 / % possible obs: 99.6 % / Redundancy: 8.8 % / Biso Wilson estimate: 37 Å2 / CC1/2: 0.995 / Rrim(I) all: 0.193 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.2→2.33 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3292 / CC1/2: 0.58 / Rrim(I) all: 1.048 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→40.583 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→40.583 Å
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Refine LS restraints |
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LS refinement shell |
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