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Yorodumi- PDB-1rxo: ACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBULOSE-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rxo | ||||||
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Title | ACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBULOSE-1,5-BISPHOSPHATE AND CALCIUM | ||||||
Components | (RIBULOSE BISPHOSPHATE CARBOXYLASE/OXYGENASE) x 2 | ||||||
Keywords | LYASE (CARBON-CARBON) | ||||||
Function / homology | Function and homology information photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / chloroplast / magnesium ion binding Similarity search - Function | ||||||
Biological species | Spinacia oleracea (spinach) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS WITH PDB ENTRY 1AUS / Resolution: 2.2 Å | ||||||
Authors | Taylor, T.C. / Andersson, I. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: The structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate. Authors: Taylor, T.C. / Andersson, I. #1: Journal: J.Mol.Biol. / Year: 1996 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rxo.cif.gz | 473.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rxo.ent.gz | 387.1 KB | Display | PDB format |
PDBx/mmJSON format | 1rxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rxo_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 1rxo_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 1rxo_validation.xml.gz | 97.2 KB | Display | |
Data in CIF | 1rxo_validation.cif.gz | 134.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rx/1rxo ftp://data.pdbj.org/pub/pdb/validation_reports/rx/1rxo | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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. |
-Components
#1: Protein | Mass: 52777.680 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / Organ: LEAF References: UniProt: P00875, ribulose-bisphosphate carboxylase #2: Protein | Mass: 14638.671 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / Organ: LEAF References: UniProt: P00870, ribulose-bisphosphate carboxylase #3: Sugar | ChemComp-RUB / #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.8 Details: 14% PEG4000, 25 MM HEPES PH 7.8, 0.2 M NACL, 10 MM CACL2; SOAKED WITH 20 MM RUBP FOR 5 DAYS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Taylor, T.C., (1996) Nat. Struct. Biol., 3, 95. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 279 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 109900 / % possible obs: 75.5 % / Redundancy: 6 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 2 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 2.8 / % possible all: 53.8 |
Reflection | *PLUS Num. measured all: 1275669 |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS WITH PDB ENTRY 1AUS Resolution: 2.2→7 Å / Isotropic thermal model: INDIVIDUAL / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.2→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: 2.2→2.3 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.27 |