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Yorodumi- PDB-7dbt: Crystal structure of catalytic domain of Anhydrobiosis-related Mn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dbt | ||||||
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Title | Crystal structure of catalytic domain of Anhydrobiosis-related Mn-dependent Peroxidase (AMNP) from Ramazzottius varieornatus (Mn2+-bound form) | ||||||
Components | AMNP/g12777 | ||||||
Keywords | OXIDOREDUCTASE / peroxidase / Manganese / tardigrade | ||||||
Function / homology | : / Conserved secreted protein Function and homology information | ||||||
Biological species | Ramazzottius varieornatus (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Yoshida, Y. / Satoh, T. / Ota, C. / Tanaka, S. / Horikawa, D.D. / Tomita, M. / Kato, K. / Arakawa, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Bmc Genomics / Year: 2022 Title: Time-series transcriptomic screening of factors contributing to the cross-tolerance to UV radiation and anhydrobiosis in tardigrades. Authors: Yoshida, Y. / Satoh, T. / Ota, C. / Tanaka, S. / Horikawa, D.D. / Tomita, M. / Kato, K. / Arakawa, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dbt.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dbt.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 7dbt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7dbt_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 7dbt_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 7dbt_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 7dbt_validation.cif.gz | 19.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/db/7dbt ftp://data.pdbj.org/pub/pdb/validation_reports/db/7dbt | HTTPS FTP |
-Related structure data
Related structure data | 7dbuSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18743.023 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ramazzottius varieornatus (invertebrata) Gene: RvY_12637-1, RvY_12637.1, RvY_12637 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D1VPD8 #2: Chemical | ChemComp-MN / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.12 Å3/Da / Density % sol: 41.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Crystallization: 10% PEG3350, 100 mM imidazole-HCl buffer (pH 7.5), 300 mM zinc acetate, and 50 mM sodium fluoride Soaking: 11% PEG3350, 100 mM imidazole-HCl buffer (pH 7.5), 50 mM manganese ...Details: Crystallization: 10% PEG3350, 100 mM imidazole-HCl buffer (pH 7.5), 300 mM zinc acetate, and 50 mM sodium fluoride Soaking: 11% PEG3350, 100 mM imidazole-HCl buffer (pH 7.5), 50 mM manganese chloride, and 50 mM sodium fluoride |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1.25 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2020 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.25 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→42.09 Å / Num. obs: 14127 / % possible obs: 98.6 % / Redundancy: 4.4 % / CC1/2: 0.987 / Rmerge(I) obs: 0.16 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1337 / CC1/2: 0.866 / % possible all: 48.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7DBU Resolution: 2.3→19.93 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.93 Å
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Refine LS restraints |
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LS refinement shell |
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