+Open data
-Basic information
Entry | Database: PDB / ID: 2ybv | ||||||
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Title | STRUCTURE OF RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS | ||||||
Components |
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Keywords | LYASE / CO2/O2 SPECIFICITY / CARBON DIOXIDE FIXATION / PHOTOSYNTHESIS / THERMOSTABILITY / PHOTORESPIRATION / MONOOXYGENASE / HYDROXYLATION / OXIDOREDUCTASE / RUBISCO / CHLOROPLAST / CALVIN CYCLE / THERMOPHILIC CYANOBACTERIA | ||||||
Function / homology | Function and homology information carboxysome / photorespiration / ribulose-bisphosphate carboxylase / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / monooxygenase activity / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | THERMOSYNECHOCOCCUS ELONGATUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Terlecka, B. / Wilhelmi, V. / Bialek, W. / Gubernator, B. / Szczepaniak, A. / Hofmann, E. | ||||||
Citation | Journal: To be Published Title: Structure of Ribulose-1,5-Bisphosphate Carboxylase Oxygenase from Thermosynechococcus Elongatus Authors: Terlecka, B. / Wilhelmi, V. / Bialek, W. / Gubernator, B. / Szczepaniak, A. / Hofmann, E. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "IB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "KB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "MB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "OB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-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 | 2ybv.cif.gz | 820.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ybv.ent.gz | 681 KB | Display | PDB format |
PDBx/mmJSON format | 2ybv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ybv_validation.pdf.gz | 562.5 KB | Display | wwPDB validaton report |
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Full document | 2ybv_full_validation.pdf.gz | 618.1 KB | Display | |
Data in XML | 2ybv_validation.xml.gz | 149 KB | Display | |
Data in CIF | 2ybv_validation.cif.gz | 207.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/2ybv ftp://data.pdbj.org/pub/pdb/validation_reports/yb/2ybv | HTTPS FTP |
-Related structure data
Related structure data | 3zxwC 3rubS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 2
NCS ensembles :
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-Components
#1: Protein | Mass: 53091.324 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) Strain: BP-1 / Plasmid: PUC18RBCLXSTH.EL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA] References: UniProt: Q8DIS5, ribulose-bisphosphate carboxylase #2: Protein | Mass: 13999.818 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) Strain: BP-1 / Plasmid: PUC18RBCLXSTH.EL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH5[ALPHA] References: UniProt: Q8DIS7, ribulose-bisphosphate carboxylase #3: Chemical | ChemComp-CL / #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: 2.72 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | pH: 7 Details: 5% PEG8000, 20% PEG200, 10% GLYCEROL, 100MM HEPES, PH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9919 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 4, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9919 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→39 Å / Num. obs: 253864 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 11.11 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.8 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RUB Resolution: 2.3→39.84 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.883 / SU B: 5.896 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.196 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→39.84 Å
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Refine LS restraints |
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