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Yorodumi- PDB-1rsc: STRUCTURE OF AN EFFECTOR INDUCED INACTIVATED STATE OF RIBULOSE BI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rsc | ||||||
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Title | STRUCTURE OF AN EFFECTOR INDUCED INACTIVATED STATE OF RIBULOSE BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE: THE BINARY COMPLEX BETWEEN ENZYME AND XYLULOSE BISPHOSPHATE | ||||||
Components |
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Keywords | LYASE (CARBON-CARBON) | ||||||
Function / homology | Function and homology information carboxysome / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | Synechococcus elongatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.3 Å | ||||||
Authors | Newman, J. / Gutteridge, S. | ||||||
Citation | Journal: Structure / Year: 1994 Title: Structure of an effector-induced inactivated state of ribulose 1,5-bisphosphate carboxylase/oxygenase: the binary complex between enzyme and xylulose 1,5-bisphosphate. Authors: Newman, J. / Gutteridge, S. #1: Journal: J.Biol.Chem. / Year: 1993 Title: The X-Ray Structure of Synechococcus Ribulose Bisphosphate Carboxylase(Slash)Oxygenase Activate Quaternary Complex at 2.2 Angstroms Resolution Authors: Newman, J. / Gutteridge, S. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: Structure Determination and Refinement of Ribulose-1,5-Bisphosphate Carboxylase(Slash)Oxygenase from Synechococcus Pcc6301 Authors: Newman, J. / Branden, C.-I. / Jones, T.A. #3: Journal: J.Biol.Chem. / Year: 1990 Title: The Purification and Preliminary X-Ray Diffraction Studies of Recombinant Synechococcus Ribulose-1,5-Bisphosphate Carboxylase(Slash)Oxygenase from E. Coli Authors: Newman, J. / Gutteridge, S. | ||||||
History |
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Remark 700 | SHEET S1 IN *SHEET RECORDS BELOW IS THE L-SUBUNIT N-TERMINAL SHEET. S2 IN *SHEET* RECORDS BELOW IS ...SHEET S1 IN *SHEET RECORDS BELOW IS THE L-SUBUNIT N-TERMINAL SHEET. S2 IN *SHEET* RECORDS BELOW IS THE L-SUBUNIT C-TERM DOMAIN SHEET. S3 IN *SHEET* RECORDS BELOW IS THE S-SUBUNIT SHEET. THIS SHEET IS +1, -2X, -1. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rsc.cif.gz | 878.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rsc.ent.gz | 726.8 KB | Display | PDB format |
PDBx/mmJSON format | 1rsc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rsc_validation.pdf.gz | 534.8 KB | Display | wwPDB validaton report |
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Full document | 1rsc_full_validation.pdf.gz | 621.6 KB | Display | |
Data in XML | 1rsc_validation.xml.gz | 97.4 KB | Display | |
Data in CIF | 1rsc_validation.cif.gz | 141.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/1rsc ftp://data.pdbj.org/pub/pdb/validation_reports/rs/1rsc | HTTPS FTP |
-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: CIS PROLINE - PRO A 176 | ||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THERE ARE 7 NON-CRYSTALLOGRAPHIC SYMMETRY OPERATORS, AND THESE MUST BE USED TO GENERATE THE ENTIRE L8S8 MOLECULE. THE FORMAT OF THE FOLLOWING TRANSFORMATIONS IS FROM X-PLOR, THUS THE SYMMETRY RELATED CHAINS ARE GENERATED BY: R'=R*R + T, R = ROTATION MATRIX, T = TRANSLATION. THESE ARE THE ROTATION/TRANSLATION COMPONENTS TO MAP AN LS MONOMER (AM) ONTO THE REST OF THE MOLECULE. THESE MATRICES WERE OBTAINED FROM X-PLOR AFTER REFINEMENT OF THE WHOLE L8S8 920710. MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX CHAIN RESIDUES CHAIN RESIDUES 1 A 9 - 475 B 9 - 475 1 M 2 - 51 I 2 - 51 1 M 59 - 122 I 59 - 122 2 A 9 - 475 C 9 - 475 2 M 2 - 51 N 2 - 51 2 M 59 - 122 N 59 - 122 3 A 9 - 475 D 9 - 475 3 M 2 - 51 J 2 - 51 3 M 59 - 122 J 59 - 122 4 A 9 - 475 E 9 - 475 4 M 2 - 51 O 2 - 51 4 M 59 - 122 O 59 - 122 5 A 9 - 475 F 9 - 475 5 M 2 - 51 F 2 - 51 5 M 59 - 122 F 59 - 122 6 A 9 - 475 G 9 - 475 6 M 2 - 51 P 2 - 51 6 M 59 - 122 P 59 - 122 7 A 9 - 475 H 9 - 475 7 M 2 - 51 L 2 - 51 7 M 59 - 122 L 59 - 122 |
-Components
#1: Protein | Mass: 52516.605 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 6301 / Cell line: S2 References: UniProt: P00880, ribulose-bisphosphate carboxylase #2: Protein | Mass: 13350.182 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 6301 / Cell line: S2 References: UniProt: P04716, ribulose-bisphosphate carboxylase #3: Sugar | ChemComp-XBP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.75 % |
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Num. obs: 145750 / % possible obs: 65 % / Num. measured all: 601269 / Rmerge(I) obs: 0.157 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.255 / Rfactor obs: 0.255 / Highest resolution: 2.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.3 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 7 Å / Num. reflection all: 141681 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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