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Yorodumi- PDB-1upm: ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL 2 BI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1upm | ||||||
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Title | ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL 2 BISPHOSPHAT AND CA2+. | ||||||
Components |
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Keywords | LYASE / CARBON-CARBON / OXIDOREDUCTASE / PHOTOSYNTHESIS / CARBON-DIOXIDE FIXATION 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 / 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: Karkehabadi, 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 | 1upm.cif.gz | 957.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1upm.ent.gz | 817.9 KB | Display | PDB format |
PDBx/mmJSON format | 1upm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1upm_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 1upm_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 1upm_validation.xml.gz | 103 KB | Display | |
Data in CIF | 1upm_validation.cif.gz | 162.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/1upm ftp://data.pdbj.org/pub/pdb/validation_reports/up/1upm | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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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.: 8 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / Tissue: LEAF References: UniProt: P00875, ribulose-bisphosphate carboxylase #2: Protein | Mass: 14638.671 Da / Num. of mol.: 8 / Source method: isolated from a natural source Details: THE COMPLETE STRUCTURE HAS BEEN SUBMITTED AS WELL AS THE MATRIX TRANSFORMATION FOR EACH CHAIN. 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: 2.6 Å3/Da / Density % sol: 40 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.8 Details: 10% PEG 4000, 0.1 M HEPES PH 7.8, 10 MM CACL2, 0.2 M NACL, 50 MM NAHCO3, 1MM 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: ID14-2 / 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→20 Å / Num. obs: 226289 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 12 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4.1 / % possible all: 70.6 |
Reflection | *PLUS Highest resolution: 2.3 Å / % possible obs: 90.2 % / Num. measured all: 2722153 / Rmerge(I) obs: 0.083 |
Reflection shell | *PLUS % possible obs: 70.6 % / Rmerge(I) obs: 0.15 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.3→20 Å / SU B: 5.994 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 4 / ESU R: 0.364 / ESU R Free: 0.21
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Displacement parameters | Biso mean: 32.408 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refinement | *PLUS Rfactor Rfree: 0.23 / Rfactor Rwork: 0.2 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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