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- PDB-5bs2: Crystal structure of RbcX-IIa from Chlamydomonas reinhardtii in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5bs2 | ||||||
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Title | Crystal structure of RbcX-IIa from Chlamydomonas reinhardtii in complex with RbcL C-terminal tail | ||||||
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![]() | CHAPERONE / RbcX | ||||||
Function / homology | ![]() ribulose bisphosphate carboxylase complex assembly / photorespiration / ribulose-bisphosphate carboxylase / carbon fixation / ribulose-bisphosphate carboxylase activity / reductive pentose-phosphate cycle / protein folding chaperone / photosynthesis / monooxygenase activity / chloroplast / magnesium ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Bracher, A. / Hauser, T. / Liu, C. / Hartl, F.U. / Hayer-Hartl, M. | ||||||
![]() | ![]() Title: Structural Analysis of the Rubisco-Assembly Chaperone RbcX-II from Chlamydomonas reinhardtii. Authors: Bracher, A. / Hauser, T. / Liu, C. / Hartl, F.U. / Hayer-Hartl, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107 KB | Display | ![]() |
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PDB format | ![]() | 82.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.2 KB | Display | ![]() |
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Full document | ![]() | 446.8 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 15 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5bs1SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 44 - 156 / Label seq-ID: 20 - 132
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Components
#1: Protein | Mass: 14917.970 Da / Num. of mol.: 2 / Fragment: UNP residues 462-473,UNP residues 44-156 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P00877, UniProt: A8HQH2, ribulose-bisphosphate carboxylase #2: Protein/peptide | | Mass: 852.030 Da / Num. of mol.: 1 / Fragment: UNP residues 462-467 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P00877, ribulose-bisphosphate carboxylase #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris-HCl pH 8.5, 25% PEG2000 MME / PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99988 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.97→49.781 Å / Num. all: 15820 / Num. obs: 15820 / % possible obs: 94.2 % / Redundancy: 2.4 % / Rpim(I) all: 0.06 / Rrim(I) all: 0.102 / Rsym value: 0.081 / Net I/av σ(I): 6.511 / Net I/σ(I): 10.4 / Num. measured all: 38750 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5BS1 Resolution: 1.97→30 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2156 / WRfactor Rwork: 0.197 / FOM work R set: 0.8017 / SU B: 11.071 / SU ML: 0.138 / SU R Cruickshank DPI: 0.2048 / SU Rfree: 0.1606 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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 max: 83.7 Å2 / Biso mean: 30.375 Å2 / Biso min: 16.36 Å2
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Refinement step | Cycle: final / Resolution: 1.97→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 5742 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.966→2.017 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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