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Yorodumi- PDB-4lms: Light harvesting complex PC645 from the cryptophyte Chroomonas sp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lms | ||||||
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Title | Light harvesting complex PC645 from the cryptophyte Chroomonas sp. CCMP270 | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / thylakoid lumen | ||||||
Function / homology | Function and homology information : / : / phycobilisome / chloroplast thylakoid membrane / photosynthesis / chloroplast Similarity search - Function | ||||||
Biological species | Chroomonas sp. (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Harrop, S.J. / Wilk, K.E. / Curmi, P.M.G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins. Authors: Harrop, S.J. / Wilk, K.E. / Dinshaw, R. / Collini, E. / Mirkovic, T. / Teng, C.Y. / Oblinsky, D.G. / Green, B.R. / Hoef-Emden, K. / Hiller, R.G. / Scholes, G.D. / Curmi, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lms.cif.gz | 242.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lms.ent.gz | 194.8 KB | Display | PDB format |
PDBx/mmJSON format | 4lms.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lms_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 4lms_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 4lms_validation.xml.gz | 33.4 KB | Display | |
Data in CIF | 4lms_validation.cif.gz | 46.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/4lms ftp://data.pdbj.org/pub/pdb/validation_reports/lm/4lms | HTTPS FTP |
-Related structure data
Related structure data | 4lm6C 4lmxC 1qgwS 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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1 |
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Unit cell |
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-Components
-Cryptophyte phycocyanin (alpha- ... , 2 types, 2 molecules AC
#1: Protein | Mass: 8733.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas sp. (eukaryote) / Strain: CCMP270 / References: UniProt: U5T880*PLUS |
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#3: Protein | Mass: 7558.731 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chroomonas sp. (eukaryote) / Strain: CCMP270 / References: UniProt: U5T8W5*PLUS |
-Protein , 1 types, 2 molecules BD
#2: Protein | Mass: 18381.947 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chroomonas sp. (eukaryote) / Strain: CCMP270 / References: UniProt: U5T8F2*PLUS |
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-Non-polymers , 5 types, 774 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CYC / #7: Chemical | #8: 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: 2.42 Å3/Da / Density % sol: 49.24 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 20% PEG4000, 20% isopropanol, 0.1 M sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.821 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 20, 2009 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.821 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→17.8 Å / Num. all: 113946 / Num. obs: 109920 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.41 / % possible all: 74.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QGW Resolution: 1.35→17.038 Å / SU ML: 0.29 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.35 / σ(I): 0 / Phase error: 17.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.015 Å2 / ksol: 0.362 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.35→17.038 Å
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Refine LS restraints |
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LS refinement shell |
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