+Open data
-Basic information
Entry | Database: PDB / ID: 2wsf | |||||||||||||||
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Title | Improved Model of Plant Photosystem I | |||||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / ELECTRON TRANSFER / MEMBRANE PROTEINS / LARGE COMPLEXES | |||||||||||||||
Function / homology | Function and homology information chloroplast photosystem I / response to low light intensity stimulus / response to high light intensity / plastoglobule / chloroplast thylakoid / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / chloroplast envelope ...chloroplast photosystem I / response to low light intensity stimulus / response to high light intensity / plastoglobule / chloroplast thylakoid / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / chloroplast envelope / photosystem I / photosynthetic electron transport in photosystem I / thylakoid / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / response to cold / chloroplast / phosphoprotein binding / 4 iron, 4 sulfur cluster binding / molecular adaptor activity / electron transfer activity / oxidoreductase activity / protein domain specific binding / mRNA binding / magnesium ion binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | ARABIDOPSIS THALIANA (thale cress) PISUM SATIVUM (garden pea) GLYCINE MAX (soybean) SPINACIA OLERACEA (spinach) HORDEUM VULGARE (barley) PHASEOLUS VULGARIS (French bean) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.48 Å | |||||||||||||||
Authors | Amunts, A. / Toporik, H. / Borovikov, A. / Nelson, N. | |||||||||||||||
Citation | Journal: J. Biol. Chem. / Year: 2010 Title: Structure determination and improved model of plant photosystem I. Authors: Amunts, A. / Toporik, H. / Borovikova, A. / Nelson, N. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wsf.cif.gz | 908.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wsf.ent.gz | 769.3 KB | Display | PDB format |
PDBx/mmJSON format | 2wsf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wsf_validation.pdf.gz | 54.9 MB | Display | wwPDB validaton report |
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Full document | 2wsf_full_validation.pdf.gz | 56.4 MB | Display | |
Data in XML | 2wsf_validation.xml.gz | 370.8 KB | Display | |
Data in CIF | 2wsf_validation.cif.gz | 417.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/2wsf ftp://data.pdbj.org/pub/pdb/validation_reports/ws/2wsf | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 5 types, 5 molecules 1234C
#1: Protein | Mass: 26021.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ARABIDOPSIS THALIANA (thale cress) / References: UniProt: Q9C5R7, UniProt: Q01667*PLUS |
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#2: Protein | Mass: 28926.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) / References: UniProt: Q41038 |
#3: Protein | Mass: 29852.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) GLYCINE MAX (soybean) / References: UniProt: C6TEX2*PLUS |
#4: Protein | Mass: 27181.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) / References: UniProt: Q9SQL2 |
#7: Protein | Mass: 8991.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) / References: UniProt: P10793 |
-PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN ... , 2 types, 2 molecules AB
#5: Protein | Mass: 84284.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) / References: UniProt: P05310 |
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#6: Protein | Mass: 82490.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) / References: UniProt: P05311 |
-PHOTOSYSTEM I REACTION CENTER SUBUNIT ... , 9 types, 9 molecules DEFGHIJKL
#8: Protein | Mass: 23170.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: P12353 |
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#9: Protein | Mass: 14984.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ARABIDOPSIS THALIANA (thale cress) / References: UniProt: Q9S831 |
#10: Protein | Mass: 25445.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: P12355 |
#11: Protein | Mass: 18232.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: P12357 |
#12: Protein | Mass: 15341.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: P22179 |
#13: Protein/peptide | Mass: 4474.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) / References: UniProt: P17227 |
#14: Protein/peptide | Mass: 5079.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: P17230 |
#15: Protein | Mass: 13742.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HORDEUM VULGARE (barley) / References: UniProt: P36886 |
#16: Protein | Mass: 22957.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SPINACIA OLERACEA (spinach) / References: UniProt: Q41385 |
-PHOTOSYSTEM I-N ... , 2 types, 2 molecules NR
#17: Protein | Mass: 18460.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PHASEOLUS VULGARIS (French bean) / References: UniProt: Q84U30 |
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#18: Protein | Mass: 4528.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PISUM SATIVUM (garden pea) |
-Sugars , 2 types, 61 molecules
#19: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose #21: Sugar | ChemComp-LMU / |
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-Non-polymers , 6 types, 196 molecules
#20: Chemical | ChemComp-CLA / #22: Chemical | ChemComp-BCR / #23: Chemical | #24: Chemical | #25: Chemical | ChemComp-LMG / | #26: Chemical | ChemComp-UNL / | Num. of mol.: 1 / Source method: obtained synthetically |
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-Details
Sequence details | SQUENCE MAPPING FOR CHAIN 3 MATCHES GB ACU20374 |
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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: 2.3 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | pH: 6 Details: 22.5 MM MES, BIS-TRIS PH 6, 10MM SUCCINIC ACID, 6% PEG6000, 0.015% DTM |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 27, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 72787 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 3.5→3.6 Å / % possible all: 78.5 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 3.48→50 Å / Cor.coef. Fo:Fc: 0.73 / Cor.coef. Fo:Fc free: 0.715 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Displacement parameters | Biso mean: 24.693 Å2
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Refinement step | Cycle: LAST / Resolution: 3.48→50 Å
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LS refinement shell | Resolution: 3.475→3.565 Å / Total num. of bins used: 20
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