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- PDB-3n90: The 1.7 Angstrom resolution crystal structure of AT2G44920, a pen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3n90 | ||||||
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Title | The 1.7 Angstrom resolution crystal structure of AT2G44920, a pentapeptide repeat protein from Arabidopsis thaliana thylakoid lumen. | ||||||
![]() | Thylakoid lumenal 15 kDa protein 1, chloroplastic | ||||||
![]() | UNKNOWN FUNCTION / right-handed quadrilateral beta helix / pentapeptide repeat protein / repeated-five residue fold / chloroplast lumen | ||||||
Function / homology | ![]() thylakoid lumen / chloroplast thylakoid / chloroplast thylakoid lumen / thylakoid / chloroplast thylakoid membrane / chloroplast / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ni, S. / Mckgookey, M. / Tinch, S.L. / Jones, A.N. / Jayaraman, S. / Kennedy, M.A. | ||||||
![]() | ![]() Title: The 1.7 Angstrom resolution crystal structure of AT2G44920, a pentapeptide repeat protein from Arabidopsis thaliana thylakoid lumen. Authors: Ni, S. / Mckgookey, M. / Tinch, S.L. / Jones, A.N. / Jayaraman, S. / Kennedy, M.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 37.6 KB | Display | ![]() |
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PDB format | ![]() | 28.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.5 KB | Display | ![]() |
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Full document | ![]() | 434.1 KB | Display | |
Data in XML | ![]() | 8.7 KB | Display | |
Data in CIF | ![]() | 11.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 16251.973 Da / Num. of mol.: 1 / Fragment: UNP residues 81-224 / Mutation: V173M, T174M Source method: isolated from a genetically manipulated source Details: T7 / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: well buffer: 2.5M ammonium sulfate, 0.5M sodium acetate; Sample buffer: 0.25M sodium chloride, 10% glycerol, 0.02M Tris, pH 7.8 protein concentration=15mg/mL, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2009 Details: Cryogenically-cooled single crystal Si(111) side bounce monochromator. Optional Si(311) to achive 13.474 keV. Vertical and horizantal focussing mirrors in Kirkpatrick-Baez geometry. |
Radiation | Monochromator: Cryogenically-cooled single crystal Si(111) side bounce monochromator. Optional Si(311) to achive 13.474 keV. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 14963 / Num. obs: 14963 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Redundancy: 1.87 % / Biso Wilson estimate: 19.93 Å2 / Rsym value: 0.081 / Net I/σ(I): 40.84 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 1.92 % / Mean I/σ(I) obs: 18.9 / Num. unique all: 2143 / Rsym value: 0.066 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 20.296 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.774 Å / Total num. of bins used: 20
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