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Yorodumi- PDB-3n90: The 1.7 Angstrom resolution crystal structure of AT2G44920, a pen... -
+Open data
-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. | ||||||
Components | Thylakoid lumenal 15 kDa protein 1, chloroplastic | ||||||
Keywords | UNKNOWN FUNCTION / right-handed quadrilateral beta helix / pentapeptide repeat protein / repeated-five residue fold / chloroplast lumen | ||||||
Function / homology | Function and homology information thylakoid lumen / chloroplast thylakoid / thylakoid / chloroplast thylakoid lumen / chloroplast thylakoid membrane / chloroplast / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Ni, S. / Mckgookey, M. / Tinch, S.L. / Jones, A.N. / Jayaraman, S. / Kennedy, M.A. | ||||||
Citation | Journal: To be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n90.cif.gz | 37.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n90.ent.gz | 28.9 KB | Display | PDB format |
PDBx/mmJSON format | 3n90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/3n90 ftp://data.pdbj.org/pub/pdb/validation_reports/n9/3n90 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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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.) Arabidopsis thaliana (thale cress) / Gene: At2g44920, T13E15.7 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: O22160 |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.662 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R Free: 0.129 / 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: 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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