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- PDB-1rco: SPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR D-XYLULOSE-2,2-DIOL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rco | ||||||
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Title | SPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR D-XYLULOSE-2,2-DIOL-1,5-BISPHOSPHATE | ||||||
![]() | (RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE) x 2 | ||||||
![]() | LYASE / CARBON-CARBON | ||||||
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. / Andersson, I. | ||||||
![]() | ![]() Title: A common structural basis for the inhibition of ribulose 1,5-bisphosphate carboxylase by 4-carboxyarabinitol 1,5-bisphosphate and xylulose 1,5-bisphosphate. Authors: Taylor, T.C. / Fothergill, M.D. / Andersson, I. #1: ![]() Title: Large Structures at High Resolution: The 1.6 A Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Complexed with 2-Carboxyarabinitol Bisphosphate Authors: 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 | ![]() | 928.3 KB | Display | ![]() |
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PDB format | ![]() | 774.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 185.3 KB | Display | |
Data in CIF | ![]() | 256.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1rboC ![]() 8rucS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE DEPOSITORS PROVIDED CHAINS L AND S. THE OTHER CHAINS TO MAKE THE COMPLETE ASYMMETRIC UNIT WERE GENERATED BY THE PROTEIN DATA BANK USING THE MTRIX TRANSFORMATIONS BELOW. |
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Components
#1: Protein | Mass: 52734.680 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P00875, ribulose-bisphosphate carboxylase #2: Protein | Mass: 14638.671 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P00870, ribulose-bisphosphate carboxylase #3: Sugar | ChemComp-XDP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.8 Details: 15% PEG 4000, 25 MM HEPES PH 7.8, 10 MM CACL2, 0.2 M NACL, 50 MM NAHCO3, 20 MM XUBP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 279 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1990 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 217862 / % possible obs: 62.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 3.4 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 1.3 / % possible all: 62.5 |
Reflection | *PLUS Num. measured all: 1519008 |
Reflection shell | *PLUS % possible obs: 62.5 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 8RUC Resolution: 2.3→7 Å / Isotropic thermal model: INDIVIDUAL / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→7 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.4 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.342 |