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Yorodumi- PDB-3l0f: High resolution structure of C-Phycocyanin from Thermosynechococc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l0f | ||||||
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Title | High resolution structure of C-Phycocyanin from Thermosynechococcus elongatus | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / PHOTOSYSTEM II / LIGHT HARVESTING PROTEINS / THERMOSTABILITY / BILE PIGMENT / CHLOROPLAST / CHROMOPHORE / ELECTRON TRANSPORT / MEMBRANE / PHYCOBILISOME / PLASTID / THYLAKOID / TRANSPORT / METHYLATION | ||||||
Function / homology | Function and homology information phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis Similarity search - Function | ||||||
Biological species | Thermosynechococcus elongatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Fromme, R. / Brune, D. / Fromme, P. | ||||||
Citation | Journal: Iucrj / Year: 2015 Title: Serial femtosecond crystallography of soluble proteins in lipidic cubic phase. Authors: Fromme, R. / Ishchenko, A. / Metz, M. / Chowdhury, S.R. / Basu, S. / Boutet, S. / Fromme, P. / White, T.A. / Barty, A. / Spence, J.C. / Weierstall, U. / Liu, W. / Cherezov, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l0f.cif.gz | 171.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l0f.ent.gz | 135.7 KB | Display | PDB format |
PDBx/mmJSON format | 3l0f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/3l0f ftp://data.pdbj.org/pub/pdb/validation_reports/l0/3l0f | HTTPS FTP |
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-Related structure data
Related structure data | 4zizC 1jboS 1ktpS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17456.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Former name Synechococcus elongatus / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P50032 | ||
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#2: Protein | Mass: 18216.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosynechococcus elongatus (bacteria) Strain: BP-1 / Gene: cpcB, tlr1957 / References: UniProt: P50033 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.45 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 8 % PEG 2000 , 0.05 M MES, 20 mM MgCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290-291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2009 / Details: Double crystal, Si(111) |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→42.79 Å / Num. all: 87205 / Num. obs: 86993 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 2.2 / Num. unique all: 12693 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1KTP and 1JBO Resolution: 1.35→19.5 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.926 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.047 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.396 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→19.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Total num. of bins used: 20
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