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Yorodumi- PDB-8ruc: ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL BISP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ruc | |||||||||
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Title | ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL BISPHOSPHATE | |||||||||
Components | (RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE) x 2 | |||||||||
Keywords | LYASE (CARBON-CARBON) / PHOTOSYNTHESIS / CARBON DIOXIDE FIXATION / PHOTORESPIRATION / LYASE / OXIDOREDUCTASE / MONOOXYGENASE / CHLOROPLAST | |||||||||
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 / MIR STARTING MODEL FOR MOLECULAR REPLACEMENT: NULL / Resolution: 1.6 Å | |||||||||
Authors | Andersson, I. / Knight, S. / Branden, C.-I. | |||||||||
Citation | 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. #1: Journal: J.Mol.Biol. / Year: 1990 Title: Crystallographic Analysis of Ribulose 1,5-Bisphosphate Carboxylase from Spinach at 2.4 A Resolution Authors: Knight, S. / Andersson, I. / Branden, C.I. #2: Journal: Nature / Year: 1989 Title: Crystal Structure of the Active Site of Ribulose-Bisphosphate Carboxylase Authors: Andersson, I. / Knight, S. / Schneider, G. / Lindqvist, Y. / Lundqvist, T. / Branden, C.-I. / Lorimer, G.H. #3: Journal: Science / Year: 1989 Title: Reexamination of the Three-Dimensional Structure of the Small Subunit of Rubisco from Higher Plants Authors: Knight, S. / Andersson, I. / Branden, C.-I. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ruc.cif.gz | 493.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ruc.ent.gz | 401.8 KB | Display | PDB format |
PDBx/mmJSON format | 8ruc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ruc_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 8ruc_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8ruc_validation.xml.gz | 97.5 KB | Display | |
Data in CIF | 8ruc_validation.cif.gz | 140.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/8ruc ftp://data.pdbj.org/pub/pdb/validation_reports/ru/8ruc | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | THE ENZYME IS A HEXADECAMER L8S8 OF EIGHT L (LARGE) SUBUNIT AND 8 S (SMALL) SUBUNITS. THE L SUBUNIT HAS BEEN ASSIGNED CHAIN IDENTIFIERS A, B, C, D, E, F, G, AND H. THE S SUBUNIT HAS BEEN ASSIGNED CHAIN IDENTIFIERS I, J, K, L, M, N, O, AND P. IN THE CATALYTICALLY COMPETENT MOLECULE, DIMERS OF THE LARGE SUBUNITS FORM FUNCTIONAL UNITS. IN REFERENCE 1 THESE DIMERS ARE DESIGNATED *AB*, *CD*, *EF*, AND *GH*. THIS ENTRY PRESENTS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONTAINS HALF THE MOLECULE: FOUR L AND FOUR S SUBUNITS RELATED BY A FOUR-FOLD AXIS THROUGH THE MOLECULAR CENTER AT X=0, Y=1/4, Z=1/4. THE FOUR L CHAINS PRESENT ARE A, C, E, G AND THE FOUR S CHAINS PRESENT ARE I, J, K, L. ALSO INCLUDED ARE FOUR MAGNESIUM IONS, FOUR INHIBITOR MOLECULES (CAP) AND 1520 WATERS. |
-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 / Source: (natural) Spinacia oleracea (spinach) / Organ: LEAF References: UniProt: P00870, ribulose-bisphosphate carboxylase #3: Chemical | ChemComp-MG / #4: Sugar | ChemComp-CAP / #5: Water | ChemComp-HOH / | Compound details | RESIDUE 201 OF THE L SUBUNITS IS A MODIFIED ACTIVATOR LYSINE WHICH IS CARBAMYLATED AT THE EPSILON- ...RESIDUE 201 OF THE L SUBUNITS IS A MODIFIED ACTIVATOR LYSINE WHICH IS CARBAMYLAT | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Andersson, I., (1983) J. Biol. Chem., 258, 14088. / PH range low: 6 / PH range high: 5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1.04 |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 7, 1990 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. obs: 277449 / Redundancy: 4 % / Rmerge(I) obs: 0.069 |
Reflection shell | Resolution: 1.6→1.67 Å / % possible all: 49 |
Reflection | *PLUS Num. measured all: 1131480 |
-Processing
Software |
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Refinement | Method to determine structure: MIR STARTING MODEL FOR MOLECULAR REPLACEMENT: NULL Resolution: 1.6→7 Å / σ(F): 0 Details: NO ELECTRON DENSITY IS OBSERVED FOR THE FIRST EIGHT RESIDUES OF THE LARGE SUBUNIT. NO COORDINATES ARE PRESENTED FOR THESE RESIDUES. THE ELECTRON DENSITY FOR RESIDUES ALA 9, SER 10 AND VAL 11 ...Details: NO ELECTRON DENSITY IS OBSERVED FOR THE FIRST EIGHT RESIDUES OF THE LARGE SUBUNIT. NO COORDINATES ARE PRESENTED FOR THESE RESIDUES. THE ELECTRON DENSITY FOR RESIDUES ALA 9, SER 10 AND VAL 11 OF THE L SUBUNITS IS WEAK.
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Displacement parameters | Biso mean: 15.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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