[English] 日本語
Yorodumi- PDB-4rku: Crystal structure of plant Photosystem I at 3 Angstrom resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rku | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of plant Photosystem I at 3 Angstrom resolution | ||||||
Components |
| ||||||
Keywords | PHOTOSYNTHESIS / light harvesting / membrane complex / plastocyanin / ferredoxin / chloroplast membrane | ||||||
Function / homology | Function and homology information plastoglobule / 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 ...plastoglobule / 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 / membrane => GO:0016020 / 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 | Mazor, Y. / Borovikova, A. / Greenberg, I. / Nelson, N. | ||||||
Citation | Journal: To be Published Title: Crystal structure of plant Photosystem I at 3.1 Angstrom resolution Authors: Mazor, Y. / Borovikova, A. / Greenberg, I. / Nelson, N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4rku.cif.gz | 1.7 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4rku.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 4rku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rku_validation.pdf.gz | 44.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4rku_full_validation.pdf.gz | 45.7 MB | Display | |
Data in XML | 4rku_validation.xml.gz | 311.5 KB | Display | |
Data in CIF | 4rku_validation.cif.gz | 354.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/4rku ftp://data.pdbj.org/pub/pdb/validation_reports/rk/4rku | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 80079.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P05310, photosystem I |
---|---|
#2: Protein | Mass: 82275.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P05311, photosystem I |
-Protein , 3 types, 3 molecules CN2
#3: Protein | Mass: 8860.276 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P10793, photosystem I |
---|---|
#13: Protein | Mass: 9740.071 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9K7 |
#15: Protein | Mass: 21974.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q41038 |
-Photosystem I reaction center subunit ... , 9 types, 9 molecules DEFGHIJKL
#4: Protein | Mass: 15348.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9K8*PLUS |
---|---|
#5: Protein | Mass: 7184.022 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9K6*PLUS |
#6: Protein | Mass: 17027.770 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: A0A0H2UKZ4*PLUS |
#7: Protein | Mass: 9083.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P20120*PLUS |
#8: Protein | Mass: 8895.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9K9*PLUS |
#9: Protein/peptide | Mass: 2798.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P17227 |
#10: Protein/peptide | Mass: 4455.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: D5MAL3 |
#11: Protein | Mass: 7260.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9L3 |
#12: Protein | Mass: 17312.748 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9L1*PLUS |
-Chlorophyll a-b binding protein ... , 3 types, 3 molecules 134
#14: Protein | Mass: 20096.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: E1C9L2*PLUS |
---|---|
#16: Protein | Mass: 29634.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q32904 |
#17: Protein | Mass: 21779.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q9SQL2 |
-Sugars , 1 types, 1 molecules
#24: Sugar | ChemComp-DGD / |
---|
-Non-polymers , 10 types, 199 molecules
#18: Chemical | #19: Chemical | ChemComp-BCR / #20: Chemical | ChemComp-LHG / #21: Chemical | ChemComp-CLA / #22: Chemical | #23: Chemical | ChemComp-CL0 / | #25: Chemical | #26: Chemical | ChemComp-LUT / ( #27: Chemical | ChemComp-NEX / ( | #28: Chemical | ChemComp-G3P / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.07 Å3/Da / Density % sol: 69.77 % |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 10, 2009 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2.534→129.642 Å / Num. all: 192138 / Num. obs: 116008 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.1 % / Biso Wilson estimate: 65.2 Å2 / Rmerge(I) obs: 0.158 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→39.693 Å / SU ML: 0.49 / σ(F): 1.34 / Phase error: 32.98 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→39.693 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 14.6315 Å / Origin y: 2.3519 Å / Origin z: 66.4733 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: ALL |