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Yorodumi- PDB-7t89: Light harvesting complex Phycocyanin PC577 from the cryptophyte H... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7t89 | ||||||||||||
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Title | Light harvesting complex Phycocyanin PC577 from the cryptophyte Hemiselmis pacifica CCMP 706 | ||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / photosynthesis light harvesting | ||||||||||||
Function / homology | Function and homology information phycobilisome / plastid / chloroplast thylakoid membrane / photosynthesis Similarity search - Function | ||||||||||||
Biological species | Hemiselmis pacifica (eukaryote) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | ||||||||||||
Authors | Michie, K.A. / Curmi, P.C. / Harrop, S. / Rathbone, H.W. | ||||||||||||
Funding support | Australia, United States, 3items
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Citation | Journal: Protein Sci. / Year: 2023 Title: Molecular structures reveal the origin of spectral variation in cryptophyte light harvesting antenna proteins. Authors: Michie, K.A. / Harrop, S.J. / Rathbone, H.W. / Wilk, K.E. / Teng, C.Y. / Hoef-Emden, K. / Hiller, R.G. / Green, B.R. / Curmi, P.M.G. #1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D. #2: Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t89.cif.gz | 425.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t89.ent.gz | 302.1 KB | Display | PDB format |
PDBx/mmJSON format | 7t89.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7t89_validation.pdf.gz | 4.7 MB | Display | wwPDB validaton report |
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Full document | 7t89_full_validation.pdf.gz | 4.8 MB | Display | |
Data in XML | 7t89_validation.xml.gz | 36.8 KB | Display | |
Data in CIF | 7t89_validation.cif.gz | 51.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/7t89 ftp://data.pdbj.org/pub/pdb/validation_reports/t8/7t89 | HTTPS FTP |
-Related structure data
Related structure data | 7t7uC 7t8sC 4lmsS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 6581.592 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hemiselmis pacifica (eukaryote) / References: UniProt: A0A067XP79 #2: Protein | Mass: 18303.785 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hemiselmis pacifica (eukaryote) / References: UniProt: A0A067XP89 #3: Chemical | ChemComp-CYC / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.56 Å3/Da / Density % sol: 52.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 10K, 15-25% 100 mM HEPES, pH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953698 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 19, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953698 Å / Relative weight: 1 |
Reflection | Resolution: 1→22.28 Å / Num. obs: 253580 / % possible obs: 93.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 8.69 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.049 / Rrim(I) all: 0.078 / Χ2: 0.97 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.02→1.04 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.372 / Num. unique obs: 7164 / CC1/2: 0.778 / Rpim(I) all: 0.33 / Χ2: 0.9 / % possible all: 58.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LMS Resolution: 1→22.28 Å / SU ML: 0.0734 / Cross valid method: FREE R-VALUE / σ(F): 0.14 / Phase error: 12.3672 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→22.28 Å
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Refine LS restraints |
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LS refinement shell |
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