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Yorodumi- PDB-5o7m: Single-shot pink beam serial crystallography: Phycocyanin (One ch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o7m | |||||||||
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Title | Single-shot pink beam serial crystallography: Phycocyanin (One chip, chip_1) | |||||||||
Components |
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Keywords | PHOTOSYNTHESIS / Phycocyanin / Serial Crystallography / Pink beam | |||||||||
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: 2.46 Å | |||||||||
Authors | Meents, A. / Oberthuer, D. / Lieske, J. / Srajer, V. / Sarrou, I. | |||||||||
Citation | Journal: Nat Commun / Year: 2017 Title: Pink-beam serial crystallography. Authors: Meents, A. / Wiedorn, M.O. / Srajer, V. / Henning, R. / Sarrou, I. / Bergtholdt, J. / Barthelmess, M. / Reinke, P.Y.A. / Dierksmeyer, D. / Tolstikova, A. / Schaible, S. / Messerschmidt, M. / ...Authors: Meents, A. / Wiedorn, M.O. / Srajer, V. / Henning, R. / Sarrou, I. / Bergtholdt, J. / Barthelmess, M. / Reinke, P.Y.A. / Dierksmeyer, D. / Tolstikova, A. / Schaible, S. / Messerschmidt, M. / Ogata, C.M. / Kissick, D.J. / Taft, M.H. / Manstein, D.J. / Lieske, J. / Oberthuer, D. / Fischetti, R.F. / Chapman, H.N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o7m.cif.gz | 197.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o7m.ent.gz | 163.1 KB | Display | PDB format |
PDBx/mmJSON format | 5o7m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5o7m_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5o7m_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5o7m_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 5o7m_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/5o7m ftp://data.pdbj.org/pub/pdb/validation_reports/o7/5o7m | HTTPS FTP |
-Related structure data
Related structure data | 5mjlC 5mjmC 5mjpC 5mjqC 1jboS 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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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 Source: (natural) Thermosynechococcus elongatus (strain BP-1) (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 natural source Source: (natural) Thermosynechococcus elongatus (strain BP-1) (bacteria) Strain: BP-1 / 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: 2.76 Å3/Da / Density % sol: 55.36 % |
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Crystal grow | Temperature: 293 K / Method: small tubes / pH: 6.4 Details: PC was crystallized in 1.5 M Ammonium Sulfate solution, 25 mM MES pH 6.4. The protein crystals appear overnight in 1 mm inner diameter capillaries. The PC crystals size (30 to 40 um) is ...Details: PC was crystallized in 1.5 M Ammonium Sulfate solution, 25 mM MES pH 6.4. The protein crystals appear overnight in 1 mm inner diameter capillaries. The PC crystals size (30 to 40 um) is correlated to the protein concentration, which varied between 10-15 mg/ml. |
-Data collection
Diffraction | Mean temperature: 293 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.15-1.25 | |||||||||
Detector | Type: RAYONIX MX340-HS / Detector: CCD / Date: Jul 9, 2016 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.46→100 Å / Num. obs: 8931 / % possible obs: 60.02 % / Observed criterion σ(F): 3 / Redundancy: 11.7 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 47.57 | |||||||||
Reflection shell | Resolution: 2.46→2.57 Å / Redundancy: 11.83 % / Num. unique obs: 462 / % possible all: 25.16 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JBO Resolution: 2.46→14.917 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.55 / Phase error: 14.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.46→14.917 Å
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Refine LS restraints |
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LS refinement shell |
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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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