+Open data
-Basic information
Entry | Database: PDB / ID: 4f0h | ||||||
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Title | UNACTIVATED RUBISCO with OXYGEN BOUND | ||||||
Components |
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Keywords | LYASE / ALPHA BETA DOMAIN / CATALYTIC DOMAIN TIM BARREL / CARBOXYLASE/OXYGENASE / NITROSYLATION / CHLOROPLAST | ||||||
Function / homology | Function and homology information ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / chloroplast / magnesium ion binding Similarity search - Function | ||||||
Biological species | Galdieria sulphuraria (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Stec, B. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structural mechanism of RuBisCO activation by carbamylation of the active site lysine. Authors: Stec, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f0h.cif.gz | 138 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f0h.ent.gz | 106.6 KB | Display | PDB format |
PDBx/mmJSON format | 4f0h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4f0h_validation.pdf.gz | 457.6 KB | Display | wwPDB validaton report |
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Full document | 4f0h_full_validation.pdf.gz | 465.2 KB | Display | |
Data in XML | 4f0h_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 4f0h_validation.cif.gz | 39.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/4f0h ftp://data.pdbj.org/pub/pdb/validation_reports/f0/4f0h | HTTPS FTP |
-Related structure data
Related structure data | 4f0kC 4f0mC 3rubS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 55111.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) References: UniProt: P23755, ribulose-bisphosphate carboxylase | ||
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#2: Protein | Mass: 16226.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Galdieria sulphuraria (eukaryote) References: UniProt: P23756, ribulose-bisphosphate carboxylase | ||
#3: Chemical | ChemComp-OXY / | ||
#4: Chemical | #5: 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: 1.98 Å3/Da / Density % sol: 38.02 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: 0.05 M potassium phosphate, 26% Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 27, 2003 / Details: confocal |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. all: 41587 / Num. obs: 37497 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.96→2.01 Å / Rmerge(I) obs: 0.33 / % possible all: 71 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RUB Resolution: 1.96→40 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.902 / SU B: 4.237 / SU ML: 0.115 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.166 / 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: 16.937 Å2
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Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.958→2.008 Å / Total num. of bins used: 20
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