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Yorodumi- PDB-3pw9: Structural and functional Analysis of Arabidopsis thaliana thylak... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pw9 | ||||||
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Title | Structural and functional Analysis of Arabidopsis thaliana thylakoid lumen protein AtTLP18.3 | ||||||
Components | UPF0603 protein At1g54780, chloroplastic | ||||||
Keywords | HYDROLASE / TAP domain / Rossmann Fold / Acid phosphatase / Phosphoamino acid binding / Thylakoid lumen membrane | ||||||
Function / homology | Function and homology information photosystem II repair / thylakoid lumen / chloroplast thylakoid / thylakoid / acid phosphatase activity / chloroplast thylakoid membrane / chloroplast / mRNA binding / nucleus Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å | ||||||
Authors | Wu, H.Y. / Liu, M.S. / Lin, T.P. / Cheng, Y.S. | ||||||
Citation | Journal: Plant Physiol. / Year: 2011 Title: Structural and functional assays of AtTLP18.3 identify its novel acid phosphatase activity in thylakoid lumen Authors: Wu, H.Y. / Liu, M.S. / Lin, T.P. / Cheng, Y.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pw9.cif.gz | 47.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pw9.ent.gz | 32.4 KB | Display | PDB format |
PDBx/mmJSON format | 3pw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pw/3pw9 ftp://data.pdbj.org/pub/pdb/validation_reports/pw/3pw9 | HTTPS FTP |
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-Related structure data
Related structure data | 3ptjC 3pvhSC C: citing same article (ref.) 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
#1: Protein | Mass: 16649.684 Da / Num. of mol.: 1 / Fragment: Phosphatase domain, UNP residues 84-235 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: cv. Columbia / Gene: At1g54780, T22H22.19 / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZVL6 | ||
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#2: Chemical | ChemComp-SER / | ||
#3: Chemical | ChemComp-CA / | ||
#4: Chemical | #5: 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: 2.68 Å3/Da / Density % sol: 54.05 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate (pH 6.5), 25-30% (w/v) Polyethylene glycol 4000 , VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2010 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→30 Å / Num. obs: 10968 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 26.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3PVH Resolution: 2.1→25.5 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 60.5851 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→25.5 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Xplor file |
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