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Yorodumi- PDB-5wse: Crystal structure of a cupin protein (tm1459) in osmium (Os) subs... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wse | |||||||||
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Title | Crystal structure of a cupin protein (tm1459) in osmium (Os) substituted form I | |||||||||
Components | Uncharacterized protein tm1459 | |||||||||
Keywords | METAL BINDING PROTEIN / cupin fold / artificial metalloenzyme / metal binding / 4 histidine motif / Osmium / Os / Platinum group metal | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Thermotoga maritima (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å | |||||||||
Authors | Fujieda, N. / Nakano, T. / Taniguchi, Y. / Ichihashi, H. / Nishikawa, Y. / Kurisu, G. / Itoh, S. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2017 Title: A Well-Defined Osmium-Cupin Complex: Hyperstable Artificial Osmium Peroxygenase Authors: Fujieda, N. / Nakano, T. / Taniguchi, Y. / Ichihashi, H. / Sugimoto, H. / Morimoto, Y. / Nishikawa, Y. / Kurisu, G. / Itoh, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wse.cif.gz | 220.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wse.ent.gz | 175.9 KB | Display | PDB format |
PDBx/mmJSON format | 5wse.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wse_validation.pdf.gz | 453.4 KB | Display | wwPDB validaton report |
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Full document | 5wse_full_validation.pdf.gz | 456.7 KB | Display | |
Data in XML | 5wse_validation.xml.gz | 24.5 KB | Display | |
Data in CIF | 5wse_validation.cif.gz | 35.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/5wse ftp://data.pdbj.org/pub/pdb/validation_reports/ws/5wse | HTTPS FTP |
-Related structure data
Related structure data | 5wsdC 5wsfC 1vj2S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13459.369 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria) Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1459, Tmari_1465 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1H0, UniProt: R4P0Z5*PLUS #2: Chemical | ChemComp-OS / #3: Water | ChemComp-HOH / | |
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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: 1.84 Å3/Da / Density % sol: 36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 25% w/v polyethylene glycol 1500, 0.1M MES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: May 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→50 Å / Num. obs: 147917 / % possible obs: 94.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.12→1.14 Å / Redundancy: 4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.7 / CC1/2: 0.847 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1vj2 Resolution: 1.12→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
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Refine analyze | Num. disordered residues: 169 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3943.2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.12→50 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.12 Å /
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