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Yorodumi- PDB-5ziq: Crystal structure of hexacoordinated heme protein from anhydrobio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ziq | ||||||
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Title | Crystal structure of hexacoordinated heme protein from anhydrobiotic tardigrade at pH 4 | ||||||
Components | Globin protein | ||||||
Keywords | OXYGEN TRANSPORT / Globin / Tardigrade / UNKNOWN FUNCTION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ramazzottius varieornatus (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Kim, J. / Fukuda, Y. / Inoue, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: FEBS J. / Year: 2019 Title: Crystal structure of Kumaglobin: a hexacoordinated heme protein from an anhydrobiotic tardigrade, Ramazzottius varieornatus. Authors: Kim, J. / Fukuda, Y. / Inoue, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ziq.cif.gz | 325 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ziq.ent.gz | 266.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ziq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/5ziq ftp://data.pdbj.org/pub/pdb/validation_reports/zi/5ziq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 20268.951 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ramazzottius varieornatus (invertebrata) Gene: RvY_09119-1, RvY_09119.1, RvY_09119 / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A1D1V896 #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: 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: 1.87 Å3/Da / Density % sol: 34.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: PEG 4000, ammonium sulfate, sodium acetate |
-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: Oct 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50.01 Å / Num. obs: 91088 / % possible obs: 96.9 % / Redundancy: 2 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 23.01 |
Reflection shell | Resolution: 1.5→1.53 Å / CC1/2: 0.838 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→50.01 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.113 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.082
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.445 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→50.01 Å
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Refine LS restraints |
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