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Yorodumi- PDB-5oya: Unusual posttranslational modifications revealed in crystal struc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oya | ||||||
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Title | Unusual posttranslational modifications revealed in crystal structures of diatom Rubisco. | ||||||
Components |
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Keywords | LYASE / PHOTOSYNTHESIS / CARBON DIOXIDE FIXATION / PHOTORESPIRATION | ||||||
Function / homology | Function and homology information ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / plastid / photosynthesis / monooxygenase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | Chaetoceros socialis (Diatom) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Valegard, K. / Andersson, I. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: Structural and functional analyses of Rubisco from arctic diatom species reveal unusual posttranslational modifications. Authors: Valegard, K. / Andralojc, P.J. / Haslam, R.P. / Pearce, F.G. / Eriksen, G.K. / Madgwick, P.J. / Kristoffersen, A.K. / van Lun, M. / Klein, U. / Eilertsen, H.C. / Parry, M.A.J. / Andersson, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oya.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5oya.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 5oya.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/5oya ftp://data.pdbj.org/pub/pdb/validation_reports/oy/5oya | HTTPS FTP |
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-Related structure data
Related structure data | 5mz2SC 5n9zC 6ftlC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Rubisco large ... , 2 types, 8 molecules ABDEFGHC
#1: Protein | Mass: 54490.707 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Chaetoceros socialis (Diatom) / References: UniProt: A0A3B6UEF4*PLUS #2: Protein | | Mass: 54474.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros socialis (Diatom) / References: UniProt: A0A3B6UEF4*PLUS |
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-Protein / Sugars , 2 types, 16 molecules IJKLMNOP
#3: Protein | Mass: 15914.852 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Chaetoceros socialis (Diatom) / References: UniProt: A0A3B6UEF5*PLUS #5: Sugar | ChemComp-CAP / |
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-Non-polymers , 3 types, 2974 molecules
#4: Chemical | ChemComp-MG / #6: Chemical | ChemComp-EDO / #7: 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: 2.49 Å3/Da / Density % sol: 50.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M Tris pH 7.5, 5%PGA, 15%PEG4000 |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96863 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96863 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→49.19 Å / Num. obs: 470418 / % possible obs: 96.1 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 6.58 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 1.49 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MZ2 Resolution: 1.8→49.19 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.867 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 27.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→49.19 Å
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Refine LS restraints |
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