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Yorodumi- PDB-3def: Crystal structure of Toc33 from Arabidopsis thaliana, dimerizatio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3def | ||||||
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Title | Crystal structure of Toc33 from Arabidopsis thaliana, dimerization deficient mutant R130A | ||||||
Components | T7I23.11 protein | ||||||
Keywords | HYDROLASE / chloroplast / Toc33 / GTPase | ||||||
Function / homology | Function and homology information protein targeting to chloroplast / chloroplast outer membrane / protein-transporting ATPase activity / chloroplast envelope / chloroplast / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / intracellular protein transport / GTPase activity / GTP binding / protein homodimerization activity ...protein targeting to chloroplast / chloroplast outer membrane / protein-transporting ATPase activity / chloroplast envelope / chloroplast / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / intracellular protein transport / GTPase activity / GTP binding / protein homodimerization activity / extracellular region / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Koenig, P. / Schleiff, E. / Sinning, I. / Tews, I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: On the significance of Toc-GTPase homodimers Authors: Koenig, P. / Oreb, M. / Rippe, K. / Muhle-Goll, C. / Sinning, I. / Schleiff, E. / Tews, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3def.cif.gz | 71 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3def.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 3def.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/3def ftp://data.pdbj.org/pub/pdb/validation_reports/de/3def | HTTPS FTP |
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-Related structure data
Related structure data | 3bb3S 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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Details | AUTHOR STATES THAT THE BIOLOGICAL UNIT IS UNKNOWN. |
-Components
#1: Protein | Mass: 29129.373 Da / Num. of mol.: 1 / Fragment: GTP-domain, UNP residues 1-251 / Mutation: R130A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: T7I23.11 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O23680, small monomeric GTPase |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GDP / |
#4: 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: 2.46 Å3/Da / Density % sol: 50.06 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 20% PEG 3350, 0.2M NH4Cl, 20% Glycerol, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 29, 2007 / Details: Toroidal Zerodur mirror |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→30 Å / Num. all: 21984 / Num. obs: 21395 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.037 / Net I/σ(I): 37.2 |
Reflection shell | Resolution: 1.96→1.99 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 1052 / Rsym value: 0.284 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3BB3 Resolution: 1.96→27.78 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.932 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.142 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.652 Å2
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Refine analyze | Luzzati coordinate error obs: 0.203 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→27.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→1.99 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -21.9992 Å / Origin y: 16.439 Å / Origin z: 0.3944 Å
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