+Open data
-Basic information
Entry | Database: PDB / ID: 6zxs | |||||||||
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Title | Cold grown Pea Photosystem I | |||||||||
Components |
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Keywords | PHOTOSYNTHESIS | |||||||||
Function / homology | Function and homology information plastoglobule / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane ...plastoglobule / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosystem I / photosystem II / 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 / metal ion binding Similarity search - Function | |||||||||
Biological species | Pisum sativum (garden pea) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Caspy, I. / Borovikova-Sheinker, A. / Subramanyam, R. / Nelson, N. | |||||||||
Funding support | Israel, India, 2items
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Citation | Journal: To Be Published Title: Structure of cold grown pea Photosystem I Authors: Nelson, N. / Caspy, I. / Subramanyam, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6zxs.cif.gz | 2.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6zxs.ent.gz | 1.6 MB | Display | PDB format |
PDBx/mmJSON format | 6zxs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zxs_validation.pdf.gz | 46.6 MB | Display | wwPDB validaton report |
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Full document | 6zxs_full_validation.pdf.gz | 46.7 MB | Display | |
Data in XML | 6zxs_validation.xml.gz | 246.4 KB | Display | |
Data in CIF | 6zxs_validation.cif.gz | 280.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/6zxs ftp://data.pdbj.org/pub/pdb/validation_reports/zx/6zxs | HTTPS FTP |
-Related structure data
Related structure data | 5l8rS 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
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 82571.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: A0A0F6NFW5, photosystem I |
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#2: Protein | Mass: 82381.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: A0A0F6NGI2, photosystem I |
-Protein , 7 types, 7 molecules CDEGL12
#3: Protein | Mass: 8860.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: P10793, photosystem I |
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#4: Protein | Mass: 16041.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS |
#5: Protein | Mass: 7479.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS |
#7: Protein | Mass: 10678.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS |
#12: Protein | Mass: 16564.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: E1C9L1 |
#13: Protein | Mass: 21335.439 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS |
#14: Protein | Mass: 22845.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: Q41038 |
-Photosystem I reaction center subunit ... , 5 types, 5 molecules FHIJK
#6: Protein | Mass: 17137.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: A0A0M3KL12 |
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#8: Protein | Mass: 9491.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: A0A0M3KL10 |
#9: Protein/peptide | Mass: 3296.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: P17227 |
#10: Protein/peptide | Mass: 4767.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: D5MAL3 |
#11: Protein | Mass: 7988.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: E1C9L3 |
-Chlorophyll a-b binding protein ... , 2 types, 2 molecules 34
#15: Protein | Mass: 24139.521 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: Q32904 |
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#16: Protein | Mass: 21994.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Variant: CBS / References: UniProt: Q9SQL2 |
-Sugars , 2 types, 14 molecules
#23: Sugar | ChemComp-LMT / #26: Sugar | ChemComp-DGD / |
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-Non-polymers , 13 types, 226 molecules
#17: Chemical | ChemComp-CL0 / | ||||||||||||||||||||||
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#18: Chemical | ChemComp-CLA / #19: Chemical | #20: Chemical | #21: Chemical | ChemComp-BCR / #22: Chemical | ChemComp-LHG / #24: Chemical | ChemComp-LMG / #25: Chemical | #27: Chemical | #28: Chemical | ChemComp-ZEX / ( | #29: Chemical | ChemComp-LUT / ( #30: Chemical | ChemComp-CHL / #31: Chemical | |
-Details
Has ligand of interest | N |
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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: 5.73 Å3/Da / Density % sol: 78.54 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: di-potassium phosphate, Tris, PEG400, glycerol, L-glutathione, octyl glucose neopentyl glycol |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Aug 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 162077 / % possible obs: 98.8 % / Redundancy: 7 % / Biso Wilson estimate: 96.13 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.326 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 3→3.05 Å / Num. unique obs: 7998 / CC1/2: 0.066 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5L8R Resolution: 3→49.63 Å / SU ML: 0.4895 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.3856 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: 123.94 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→49.63 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: 14.8200063301 Å / Origin y: 7.42920184276 Å / Origin z: -42.0413916319 Å
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Refinement TLS group | Selection details: all |