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Open data
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Basic information
Entry | Database: PDB / ID: 1gk8 | ||||||
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Title | Rubisco from Chlamydomonas reinhardtii | ||||||
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![]() | LYASE / RUBISCO / PHOTOSYNTHESIS | ||||||
Function / homology | ![]() photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / chloroplast / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Taylor, T.C. | ||||||
![]() | ![]() Title: First Crystal Structure of Rubisco from a Green Alga, Chlamydomonas Reinhardtii. Authors: Taylor, T.C. / Backlund, A. / Bjorhall, K. / Spreitzer, R.J. / Andersson, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 526.2 KB | Display | ![]() |
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PDB format | ![]() | 430.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 114.6 KB | Display | |
Data in CIF | ![]() | 167.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8rucS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 2 types, 8 molecules ACEGIKMO
#1: Protein | Mass: 52696.840 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P00877, ribulose-bisphosphate carboxylase #2: Protein | Mass: 16283.806 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P00873, ribulose-bisphosphate carboxylase |
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-Sugars , 1 types, 4 molecules ![](data/chem/img/CAP.gif)
#4: Sugar | ChemComp-CAP / |
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-Non-polymers , 3 types, 2593 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-MG / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUE 46 IN THE LARGE SUBUNITS (CHAIN A C E G) WAS FOUND TO BE PRO AFTER INSPECTION OF THE ...RESIDUE 46 IN THE LARGE SUBUNITS (CHAIN A C E G) WAS FOUND TO BE PRO AFTER INSPECTION |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.21 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / pH: 7.5 Details: 50 MM HEPES PH 7.5, 8-12% PEG 4000, 50 MM NAHCO3, 5 MM MGCL2, 50 UM 2-CABP, 18 DEG C, 10-15 MG/ML PROTEIN | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Date: Jun 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→100 Å / Num. obs: 469880 / % possible obs: 97 % / Redundancy: 4 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.4→1.43 Å / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 2.6 / % possible all: 94 |
Reflection | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 100 Å / Num. obs: 30387 / % possible obs: 97 % / Num. measured all: 469880 |
Reflection shell | *PLUS Highest resolution: 1.4 Å / % possible obs: 94 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 8RUC Resolution: 1.4→20 Å / SU B: 9.7 / SU ML: 0.38 / Cross valid method: THROUGHOUT / ESU R Free: 0.05 Details: CONTRIBUTION FOR RIDING HYDROGENS ADDED DURING LAST CYCLE. THE SMALL SUBUNIT C TERMINUS IS DISORDERED BEYOND RESIDUE 126. THE LARGE SUBUNIT N-TERMINI ARE DISORDERED.
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Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 13.1 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS
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