+Open data
-Basic information
Entry | Database: PDB / ID: 6hqb | ||||||
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Title | Monomeric cyanobacterial photosystem I | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / Crystal structure / Cyanobacteria / Membrane complexes / Photosystem I / Synechocystis | ||||||
Function / homology | Function and homology information plasma membrane-derived photosystem I / photosystem I reaction center / photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity ...plasma membrane-derived photosystem I / photosystem I reaction center / photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Synechocystis sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å | ||||||
Authors | Netzer-El, S.Y. / Nelson, N. / Caspy, I. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: Front Plant Sci / Year: 2018 Title: Crystal Structure of Photosystem I Monomer From Synechocystis PCC 6803. Authors: Netzer-El, S.Y. / Caspy, I. / Nelson, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hqb.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6hqb.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 6hqb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hqb_validation.pdf.gz | 26.7 MB | Display | wwPDB validaton report |
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Full document | 6hqb_full_validation.pdf.gz | 27.1 MB | Display | |
Data in XML | 6hqb_validation.xml.gz | 144.9 KB | Display | |
Data in CIF | 6hqb_validation.cif.gz | 173.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hq/6hqb ftp://data.pdbj.org/pub/pdb/validation_reports/hq/6hqb | 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
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 83036.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa / References: UniProt: P29254, photosystem I |
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#2: Protein | Mass: 81369.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa / References: UniProt: P29255, photosystem I |
-Photosystem I reaction center subunit ... , 8 types, 8 molecules DEFIJKLM
#4: Protein | Mass: 15663.749 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa / References: UniProt: P19569 |
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#5: Protein | Mass: 7680.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa / References: UniProt: P12975 |
#6: Protein | Mass: 15791.086 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa / References: UniProt: P29256 |
#7: Protein/peptide | Mass: 4414.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa / References: UniProt: Q55330 |
#8: Protein/peptide | Mass: 4535.415 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa / References: UniProt: Q55329 |
#9: Protein | Mass: 7339.811 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa / References: UniProt: P74564 |
#10: Protein | Mass: 14523.503 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa / References: UniProt: P37277 |
#11: Protein/peptide | Mass: 3382.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa / References: UniProt: P72986 |
-Protein / Sugars , 2 types, 2 molecules C
#24: Sugar | ChemComp-LMT / |
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#3: Protein | Mass: 8706.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) Strain: PCC 6803 / Kazusa / References: UniProt: P32422, photosystem I |
-Non-polymers , 13 types, 129 molecules
#12: Chemical | ChemComp-CLA / #13: Chemical | #14: Chemical | #15: Chemical | ChemComp-BCR / #16: Chemical | ChemComp-LHG / #17: Chemical | ChemComp-45D / | #18: Chemical | ChemComp-CL / | #19: Chemical | #20: Chemical | #21: Chemical | #22: Chemical | #23: Chemical | #25: Chemical | ChemComp-EQ3 / ( | |
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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: 3.35 Å3/Da / Density % sol: 69.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: KCl, MES-NaOH, PEG 3350, sulfoquinovosyldiacylglycerol or Jeffamine M-600 |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 4→50 Å / Num. obs: 34852 / % possible obs: 99.7 % / Redundancy: 24 % / Rpim(I) all: 0.092 / Net I/σ(I): 4.9 | |||||||||||||||
Reflection shell | Resolution: 4→50 Å / Rpim(I) all: 0.437 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→49.289 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.87 / 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→49.289 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -40.0247 Å / Origin y: -23.0823 Å / Origin z: -34.8269 Å
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Refinement TLS group | Selection details: all |