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Yorodumi- PDB-3bb4: Crystal structure of Toc33 from Arabidopsis thaliana in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bb4 | ||||||
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Title | Crystal structure of Toc33 from Arabidopsis thaliana in complex with Mg2+ and GMPPNP | ||||||
Components | T7I23.11 protein | ||||||
Keywords | HYDROLASE / Rossmann fold / GTPase domain / chloroplast import | ||||||
Function / homology | Function and homology information protein targeting to chloroplast / chloroplast outer membrane / protein-transporting ATPase activity / chloroplast envelope / chloroplast / intracellular protein transport / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / GTPase activity / GTP binding / protein homodimerization activity ...protein targeting to chloroplast / chloroplast outer membrane / protein-transporting ATPase activity / chloroplast envelope / chloroplast / intracellular protein transport / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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: 2.85 Å | ||||||
Authors | Koenig, P. / Sinning, I. / Schleiff, E. / Tews, I. | ||||||
Citation | Journal: Structure / Year: 2008 Title: The GTPase cycle of the chloroplast import receptors Toc33/Toc34: implications from monomeric and dimeric structures. Authors: Koenig, P. / Oreb, M. / Hofle, A. / Kaltofen, S. / Rippe, K. / Sinning, I. / Schleiff, E. / Tews, I. | ||||||
History |
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Remark 650 | DETERMINATION METHOD: AUTHOR DETERMINED | ||||||
Remark 700 | DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bb4.cif.gz | 63.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bb4.ent.gz | 45.7 KB | Display | PDB format |
PDBx/mmJSON format | 3bb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bb4_validation.pdf.gz | 749.6 KB | Display | wwPDB validaton report |
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Full document | 3bb4_full_validation.pdf.gz | 757.7 KB | Display | |
Data in XML | 3bb4_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 3bb4_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/3bb4 ftp://data.pdbj.org/pub/pdb/validation_reports/bb/3bb4 | HTTPS FTP |
-Related structure data
Related structure data | 3bb1C 3bb3C 1h65S 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: 29257.521 Da / Num. of mol.: 1 / Fragment: UNP residues 1-251 / Mutation: S181E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Columbia / Gene: T7I23.11 / Plasmid: pET21d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O23680 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GNP / |
#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: 2.71 Å3/Da / Density % sol: 54.57 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 22% PEG1500, 15% glycerol, pH7.4, VAPOR DIFFUSION, SITTING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9746 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 11, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9746 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→25 Å / Num. all: 7834 / Num. obs: 7827 / % possible obs: 99.6 % / Observed criterion σ(F): -4 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 69.8 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 15.39 |
Reflection shell | Resolution: 2.84→2.94 Å / Redundancy: 6 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2.2 / Num. unique all: 748 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H65 Resolution: 2.85→25 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.896 / SU B: 33.329 / SU ML: 0.285 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.411 / 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: 69.779 Å2
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Refine analyze | Luzzati coordinate error obs: 0.398 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.848→2.921 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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