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Yorodumi- PDB-3rub: CRYSTAL STRUCTURE OF THE UNACTIVATED FORM OF RIBULOSE-1,5-BISPHOS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rub | ||||||
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Title | CRYSTAL STRUCTURE OF THE UNACTIVATED FORM OF RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM TOBACCO REFINED AT 2.0-ANGSTROMS RESOLUTION | ||||||
Components | (RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE, FORM III) x 2 | ||||||
Keywords | LYASE(CARBON-CARBON) | ||||||
Function / homology | Function and homology information photorespiration / plasmodesma / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / chloroplast / monooxygenase activity / defense response to virus / magnesium ion binding Similarity search - Function | ||||||
Biological species | Nicotiana tabacum (common tobacco) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Schreuder, H. / Cascio, D. / Curmi, P.M.G. / Chapman, M.S. / Suh, S.W. / Eisenberg, D.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1992 Title: Crystal structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase/oxygenase from tobacco refined at 2.0-A resolution. Authors: Curmi, P.M. / Cascio, D. / Sweet, R.M. / Eisenberg, D. / Schreuder, H. #1: Journal: To be Published Title: Crystal Structure of the Inactive Form of Ribulose-1,5-Bisphosphate Carboxylase(Slash)Oxygenase (Rubis/Co): Disulfide Bonds and Active Site Region Authors: Schreuder, H. / Curmi, P.M.G. / Cascio, D. / Eisenberg, D. #2: Journal: Science / Year: 1988 Title: Tertiary Structure of Plant Rubis/Co: Domains and Their Contacts Authors: Chapman, M.S. / Suh, S.W. / Curmi, P.M.G. / Cascio, D. / Smith, W.W. / Eisenberg, D.S. #3: Journal: Nature / Year: 1987 Title: Sliding-Layer Conformational Change Limited by the Quaternary Structure of Plant Rubis/Co Authors: Chapman, M.S. / Suh, S.W. / Cascio, D. / Smith, W.W. / Eisenberg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rub.cif.gz | 126.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rub.ent.gz | 101.9 KB | Display | PDB format |
PDBx/mmJSON format | 3rub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/3rub ftp://data.pdbj.org/pub/pdb/validation_reports/ru/3rub | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Atom site foot note | 1: PRO L 176 IS A CIS PROLINE. 2: RESIDUES 90 - 96 AND 330 - 340 OF THE LARGE SUBUNIT AND RESIDUES 104 - 110 OF THE SMALL SUBUNIT HAVE VERY HIGH TEMPERATURE FACTORS. 3: MET L 405 WAS MODELED AS GLY, THEREFORE NO SIDECHAIN COORDINATES ARE PRESENTED FOR THIS RESIDUE. | ||||||||||||||||||
Components on special symmetry positions |
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-Components
#1: Protein | Mass: 53041.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nicotiana tabacum (common tobacco) References: UniProt: P00876, ribulose-bisphosphate carboxylase | ||||||
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#2: Protein | Mass: 14573.587 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source References: UniProt: P69249, ribulose-bisphosphate carboxylase | ||||||
#3: Chemical | #4: Chemical | ChemComp-ASN / | #5: Water | ChemComp-HOH / | Compound details | THERE ARE SALT BRIDGES BETWEEN THE FOLLOWING ATOMS AND SYMMETRY RELATED ATOMS. (THE 'A' AND 'D' ...THERE ARE SALT BRIDGES BETWEEN THE FOLLOWING ATOMS AND SYMMETRY RELATED ATOMS. (THE 'A' AND 'D' DENOTE ACCEPTOR AND DONOR RESPECTIVE | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.21 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.2 / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 43733 / % possible obs: 84.1 % / Rmerge(I) obs: 0.088 |
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Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.1 Å / Rmerge(I) obs: 0.214 |
-Processing
Software | Name: PROFFT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2→8 Å Details: RESIDUES 64-68 OF THE LARGE SUBUNIT ARE COMPLETELY DISORDERED. NO COORDINATES ARE PRESENTED FOR THESE RESIDUES. RESIDUES 90 - 96 AND 330 - 340 OF THE LARGE SUBUNIT AND RESIDUES 104 - 110 OF ...Details: RESIDUES 64-68 OF THE LARGE SUBUNIT ARE COMPLETELY DISORDERED. NO COORDINATES ARE PRESENTED FOR THESE RESIDUES. RESIDUES 90 - 96 AND 330 - 340 OF THE LARGE SUBUNIT AND RESIDUES 104 - 110 OF THE SMALL SUBUNIT HAVE VERY HIGH TEMPERATURE FACTORS.
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Refinement | *PLUS σ(I): 1 / Rfactor all: 0.194 / Rfactor obs: 0.171 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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