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Yorodumi- PDB-5rub: CRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF RIBULOSE-1,5-BISPHOS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5rub | |||||||||
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Title | CRYSTALLOGRAPHIC REFINEMENT AND STRUCTURE OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE FROM RHODOSPIRILLUM RUBRUM AT 1.7 ANGSTROMS RESOLUTION | |||||||||
Components | RUBISCO (RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE) | |||||||||
Keywords | LYASE(CARBON-CARBON) | |||||||||
Function / homology | Function and homology information ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Rhodospirillum rubrum (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.7 Å | |||||||||
Authors | Schneider, G. / Lindqvist, Y. / Lundqvist, T. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1990 Title: Crystallographic refinement and structure of ribulose-1,5-bisphosphate carboxylase from Rhodospirillum rubrum at 1.7 A resolution. Authors: Schneider, G. / Lindqvist, Y. / Lundqvist, T. #1: Journal: Biochemistry / Year: 1991 Title: Crystal Structure of the Ternary Complex of Ribulose-1,5-Bisphosphate Carboxylase, Mg(II), and Activator Co2 at 2.3-Angstroms Resolution Authors: Lundqvist, T. / Schneider, G. #2: Journal: J.Biol.Chem. / Year: 1989 Title: Crystal Structure of the Complex of Ribulose-1,5-Bisphosphate Carboxylase and a Transition State Analogue, 2-Carboxy-D-Arabinitol 1,5-Bisphosphate Authors: Lundqvist, T. / Schneider, G. #3: 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. #4: Journal: J.Biol.Chem. / Year: 1988 Title: Crystal Structure of the Binary Complex of Ribulose-1,5-Bisphosphate Carboxylase and its Product, 3-Phospho-D-Glycerate Authors: Lundqvist, T. / Schneider, G. #5: Journal: Embo J. / Year: 1986 Title: Three-Dimensional Structure of Ribulose-1,5-Bisphosphate Carboxylase(Slash)Oxygenase from Rhodospirillum Rubrum at 2.9 Angstroms Resolution Authors: Schneider, G. / Lindqvist, Y. / Branden, C.-I. / Lorimer, G. | |||||||||
History |
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Remark 700 | SHEET THE SHEETS PRESENTED AS *ACT* AND *BCT* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED ...SHEET THE SHEETS PRESENTED AS *ACT* AND *BCT* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA-BARRELS. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5rub.cif.gz | 194.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5rub.ent.gz | 151.3 KB | Display | PDB format |
PDBx/mmJSON format | 5rub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/5rub ftp://data.pdbj.org/pub/pdb/validation_reports/ru/5rub | HTTPS FTP |
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-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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Atom site foot note | 1: RESIDUES PRO A 167 AND PRO B 167 ARE CIS PROLINES. | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.37374, -0.056207, 0.940855), Vector: |
-Components
#1: Protein | Mass: 53268.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodospirillum rubrum (bacteria) References: UniProt: P04718, ribulose-bisphosphate carboxylase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.49 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4,20 ℃ / Method: microdialysis / PH range low: 5.8 / PH range high: 5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.7 Å / Num. obs: 76719 / Num. measured all: 183490 / Rmerge(I) obs: 0.083 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.7→5.5 Å / σ(F): 0 /
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Refinement step | Cycle: LAST / Resolution: 1.7→5.5 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 5.5 Å / Num. reflection obs: 76452 / σ(F): 1 / Rfactor obs: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 45.9 Å2 |