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Yorodumi- PDB-2o01: The Structure of a plant photosystem I supercomplex at 3.4 Angstr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o01 | |||||||||
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Title | The Structure of a plant photosystem I supercomplex at 3.4 Angstrom resolution | |||||||||
Components |
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Keywords | PHOTOSYNTHESIS / Membranal Super Complex | |||||||||
Function / homology | Function and homology information response to low light intensity stimulus / plastoglobule / response to high light intensity / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / chloroplast envelope / photosystem I reaction center / photosystem I ...response to low light intensity stimulus / plastoglobule / response to high light intensity / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / thylakoid / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / response to cold / chloroplast / phosphoprotein binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / molecular adaptor activity / protein domain specific binding / mRNA binding / magnesium ion binding / metal ion binding / nucleus / plasma membrane Similarity search - Function | |||||||||
Biological species | Pisum sativum (garden pea) Spinacia oleracea (spinach) Arabidopsis thaliana (thale cress) Phaseolus vulgaris (French bean) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å | |||||||||
Authors | Amunts, A. / Drory, O. / Nelson, N. | |||||||||
Citation | Journal: Nature / Year: 2007 Title: The structure of a plant photosystem I supercomplex at 3.4 A resolution. Authors: Amunts, A. / Drory, O. / Nelson, N. | |||||||||
History |
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Remark 650 | HELIX determination method: author determined | |||||||||
Remark 700 | SHEET determination method: author determined | |||||||||
Remark 750 | TURN determination method: author determined | |||||||||
Remark 999 | SEQUENCE Sequence for Chain K was modeled as ALA due to poor electron density, therefore alignment ...SEQUENCE Sequence for Chain K was modeled as ALA due to poor electron density, therefore alignment is unclear and residues in coordinates were labeled as UNK. Proper sequence is LGAKCDFIGSSTNLIMVTSTTLMLFAGRFGLAPSANRKATAGLRLEARDSGLQ TGDPAGFTLADTLACGTVGHIIGVGVVLGLKNIGAI |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o01.cif.gz | 810.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o01.ent.gz | 646 KB | Display | PDB format |
PDBx/mmJSON format | 2o01.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o0/2o01 ftp://data.pdbj.org/pub/pdb/validation_reports/o0/2o01 | HTTPS FTP |
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-Related structure data
Related structure data | 1qzvS 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: 83669.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Strain: alaska / References: UniProt: P05310 |
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#2: Protein | Mass: 82226.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: P05311 |
-Protein , 6 types, 6 molecules CN1234
#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 |
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#13: Protein | Mass: 9767.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phaseolus vulgaris (French bean) / References: UniProt: Q84U30 |
#14: Protein | Mass: 20415.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q01667 |
#15: Protein | Mass: 20580.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q41038 |
#16: Protein | Mass: 17929.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SY97 |
#17: Protein | Mass: 18561.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / References: UniProt: Q9SQL2 |
-Photosystem I reaction center subunit ... , 9 types, 9 molecules DEFGHIJKL
#4: Protein | Mass: 15553.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12353 |
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#5: Protein | Mass: 7127.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9S831 |
#6: Protein | Mass: 17299.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12355 |
#7: Protein | Mass: 10518.862 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P12357 |
#8: Protein | Mass: 8143.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P22179 |
#9: Protein/peptide | Mass: 3270.042 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: 4845.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P17230 |
#11: Protein/peptide | Mass: 3252.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) |
#12: Protein | Mass: 17479.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q41385 |
-Non-polymers , 4 types, 178 molecules
#18: Chemical | ChemComp-CLA / #19: Chemical | #20: Chemical | ChemComp-BCR / #21: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 10 |
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-Sample preparation
Crystal | Density Matthews: 4.15 Å3/Da / Density % sol: 70.33 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6 Details: pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.875 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.875 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. obs: 70551 / % possible obs: 91.1 % / Observed criterion σ(F): 3.4 / Observed criterion σ(I): 3.4 / Redundancy: 3.6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 16.41 |
Reflection shell | Resolution: 3.4→3.52 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 3.4 / Num. unique all: 6034 / % possible all: 78.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: PDB ENTRY 1QZV Resolution: 3.4→40 Å / Cor.coef. Fo:Fc: 0.778 / Cor.coef. Fo:Fc free: 0.707 / SU B: 34.519 / SU ML: 0.625 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.975 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.13 Å2
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Refinement step | Cycle: LAST / Resolution: 3.4→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.488 Å / Total num. of bins used: 20
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