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Yorodumi- PDB-1rbo: SPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR 2-CARBOXYARABINITOL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rbo | ||||||
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Title | SPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE | ||||||
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 8RUC / Resolution: 2.3 Å | ||||||
Authors | Taylor, T.C. / Andersson, I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1996 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: 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 | 1rbo.cif.gz | 469.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rbo.ent.gz | 399.6 KB | Display | PDB format |
PDBx/mmJSON format | 1rbo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rbo_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 1rbo_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1rbo_validation.xml.gz | 93.7 KB | Display | |
Data in CIF | 1rbo_validation.cif.gz | 133.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rb/1rbo ftp://data.pdbj.org/pub/pdb/validation_reports/rb/1rbo | 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: 52734.680 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-CAP / #4: Water | ChemComp-HOH / | |
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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: 2.31 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.4 Details: 1.7 M (NH4)2SO4, 50 MM PHOSPHATE, PH 7.4 3 MM MGCL2, 25 MM NAHCO3, 10 MM 4CABP | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS 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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.009 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1989 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.009 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 108532 / % possible obs: 90.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.3→2.36 Å / % possible all: 100 |
Reflection | *PLUS Num. measured all: 488333 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS WITH 8RUC / Resolution: 2.3→7 Å / Isotropic thermal model: INDIVIDUAL / Cross valid method: THROUGHOUT / σ(F): 2
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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: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.167 |