+Open data
-Basic information
Entry | Database: PDB / ID: 6fos | |||||||||
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Title | Cyanidioschyzon merolae photosystem I | |||||||||
Components |
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Keywords | PHOTOSYNTHESIS / membrane protein / photosynthetic complex / reaction center / photosystem | |||||||||
Function / homology | Function and homology information thylakoid membrane / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / plastid / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / response to light stimulus ...thylakoid membrane / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / plastid / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Cyanidioschyzon merolae (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4 Å | |||||||||
Authors | Nelson, N. / Hippler, M. / Antoshvili, M. / Caspy, I. | |||||||||
Funding support | Belgium, Israel, 2items
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Citation | Journal: Photosyn. Res. / Year: 2019 Title: Structure and function of photosystem I in Cyanidioschyzon merolae. Authors: Antoshvili, M. / Caspy, I. / Hippler, M. / Nelson, N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fos.cif.gz | 694.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fos.ent.gz | 572.2 KB | Display | PDB format |
PDBx/mmJSON format | 6fos.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fos_validation.pdf.gz | 33.8 MB | Display | wwPDB validaton report |
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Full document | 6fos_full_validation.pdf.gz | 34.7 MB | Display | |
Data in XML | 6fos_validation.xml.gz | 146 KB | Display | |
Data in CIF | 6fos_validation.cif.gz | 180 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/6fos ftp://data.pdbj.org/pub/pdb/validation_reports/fo/6fos | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 3 types, 4 molecules 234O
#1: Protein | Mass: 24270.199 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote) Strain: 10D / References: UniProt: M1UU36 #2: Protein | | Mass: 23987.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote) Strain: 10D / References: UniProt: M1VKK5 #14: Protein | | Mass: 10625.323 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote) Strain: 10D / References: UniProt: M1VFJ4 |
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-Photosystem I P700 chlorophyll a apoprotein ... , 3 types, 3 molecules ABD
#3: Protein | Mass: 81829.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote) Strain: 10D / References: UniProt: Q85FY7, photosystem I |
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#4: Protein | Mass: 81301.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote) Strain: 10D / References: UniProt: Q85FY6, photosystem I |
#6: Protein | Mass: 13896.780 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote) Strain: 10D / References: UniProt: Q85FY0 |
-Photosystem I iron-sulfur ... , 2 types, 2 molecules CE
#5: Protein | Mass: 8691.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote) Strain: 10D / References: UniProt: Q85G47, photosystem I |
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#7: Protein | Mass: 7890.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote) Strain: 10D / References: UniProt: Q85FZ1 |
-Photosystem I reaction center subunit ... , 6 types, 6 molecules FIJKLM
#8: Protein | Mass: 18055.459 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote) Strain: 10D / References: UniProt: Q85FS9 |
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#9: Protein/peptide | Mass: 3408.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote) Strain: 10D / References: UniProt: Q85FQ6 |
#10: Protein/peptide | Mass: 4410.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote) Strain: 10D / References: UniProt: Q85FS8 |
#11: Protein/peptide | Mass: 4820.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote) Strain: 10D / References: UniProt: Q85G51 |
#12: Protein | Mass: 15157.522 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote) Strain: 10D / References: UniProt: Q85FP8 |
#13: Protein/peptide | Mass: 3139.878 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote) Strain: 10D / References: UniProt: Q85G73 |
-Non-polymers , 4 types, 147 molecules
#15: Chemical | ChemComp-CLA / #16: Chemical | #17: Chemical | #18: Chemical | ChemComp-BCR / |
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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: 5.08 Å3/Da / Density % sol: 75.76 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 80mM MgCl2 , 50mM Citric acid, 4-7.5% PEG 4000, 0.025% alpha-DM, pH 4.8-5.0 or 80mM MgCl2 , 50mM Cacodylate, 4-7.5% PEG 4000, 0.025% alpha-DM, pH 5-6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 4→49 Å / Num. obs: 41951 / % possible obs: 80.89 % / Redundancy: 12 % / Rpim(I) all: 0.036 / Net I/σ(I): 4 |
Reflection shell | Resolution: 4→4.99 Å / Rpim(I) all: 1.236 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 4→48.53 Å / SU ML: 0.93 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 55.96 / 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: 4→48.53 Å
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Refine LS restraints |
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LS refinement shell |
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