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Yorodumi- PDB-1upp: SPINACH RUBISCO IN COMPLEX WITH 2-CARBOXYARABINITOL 2 BISPHOSPHAT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1upp | ||||||
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Title | SPINACH RUBISCO IN COMPLEX WITH 2-CARBOXYARABINITOL 2 BISPHOSPHATE and Calcium. | ||||||
Components |
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Keywords | LYASE / CARBON-CARBON / OXIDOREDUCTASE / PHOTOSYNTHESIS / CARBON-DIOXIDE FIXATION | ||||||
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 / OTHER / Resolution: 2.3 Å | ||||||
Authors | Karkehabadi, S. / Taylor, T.C. / Andersson, I. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Calcium Supports Loop Closure But not Catalysis in Rubisco Authors: Karehabadi, S. / Taylor, T.C. / Andersson, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1upp.cif.gz | 472.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1upp.ent.gz | 399.3 KB | Display | PDB format |
PDBx/mmJSON format | 1upp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1upp_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1upp_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1upp_validation.xml.gz | 59.8 KB | Display | |
Data in CIF | 1upp_validation.cif.gz | 88.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/1upp ftp://data.pdbj.org/pub/pdb/validation_reports/up/1upp | 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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-Components
#1: Protein | Mass: 52849.742 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 Details: THIS IS THE SECOND STRUCTURE OF THIS COMPLEX THAT IS BEING SUBMITTED. THE PREVOUS STRUCTURE, PDB ID CODE 1UPM, WAS OBTAINED FROM A CRYSTAL OF RUBISCO-CA COOCRYSTALLIZED WITH 2-CABP WHERAS ...Details: THIS IS THE SECOND STRUCTURE OF THIS COMPLEX THAT IS BEING SUBMITTED. THE PREVOUS STRUCTURE, PDB ID CODE 1UPM, WAS OBTAINED FROM A CRYSTAL OF RUBISCO-CA COOCRYSTALLIZED WITH 2-CABP WHERAS THIS STRUCTURE IS FROM A RUBISCO-CA/3PGA CRYSTAL WHICH WAS SOAKED WITH 2-CABP Source: (natural) SPINACIA OLERACEA (spinach) / Organ: LEAF References: UniProt: Q43832, ribulose-bisphosphate carboxylase #3: Chemical | ChemComp-CA / #4: Sugar | ChemComp-CAP / #5: Water | ChemComp-HOH / | Compound details | RUBISCO CATALYZES THE CARBOXYLATION OF D-RIBULOSE 1,5- BISPHOSPHATE AS WELL AS THE OXIDATIVE ...RUBISCO CATALYZES THE CARBOXYLAT | |
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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: 2.1 Å3/Da / Density % sol: 40 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.8 Details: 10% PEG 4000, 0.1M HEPES PH 7.8, 10 MM CACL2, 0.2 M NACL, 50 MM NAHCO3, 0.1 M 3PGA THEN SOAKED IN 2-CABP | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.8 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ESRF / Beamline: ID14-4 / Wavelength: 0.9386 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9386 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→100 Å / Num. obs: 108187 / % possible obs: 76.1 % / Observed criterion σ(I): 2 / Redundancy: 17.4 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.1→2.12 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.1 / % possible all: 70 |
Reflection | *PLUS Highest resolution: 2.1 Å / Num. obs: 108187 / % possible obs: 76.1 % / Num. measured all: 1884294 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 70 % / Rmerge(I) obs: 0.24 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.3→100 Å / SU B: 9.449 / SU ML: 0.254 / Cross valid method: THROUGHOUT / σ(F): 4 / ESU R: 0.539 / ESU R Free: 0.314 / Details: THE DATA IS FROM A MEROHEDRALLY TWINNED CRYSTAL
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Displacement parameters | Biso mean: 25.364 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→100 Å
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Refinement | *PLUS Highest resolution: 2.1 Å / Rfactor Rfree: 0.3 / Rfactor Rwork: 0.26 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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