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Yorodumi- PDB-3bb3: Crystal structure of Toc33 from Arabidopsis thaliana in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bb3 | ||||||
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Title | Crystal structure of Toc33 from Arabidopsis thaliana in complex with GDP and Mg2+ | ||||||
Components | T7I23.11 protein | ||||||
Keywords | HYDROLASE / Rossmann fold / GTPase domain / Chloroplast import / GTP-binding / Membrane / Nucleotide-binding / Outer membrane / Protein transport / Transmembrane / Transport | ||||||
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: 2.94 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 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bb3.cif.gz | 63.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bb3.ent.gz | 45.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bb3_validation.pdf.gz | 763.1 KB | Display | wwPDB validaton report |
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Full document | 3bb3_full_validation.pdf.gz | 771.4 KB | Display | |
Data in XML | 3bb3_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 3bb3_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/3bb3 ftp://data.pdbj.org/pub/pdb/validation_reports/bb/3bb3 | HTTPS FTP |
-Related structure data
Related structure data | 3bb1C 3bb4C 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: 29215.486 Da / Num. of mol.: 1 / Fragment: UNP residues 1-251 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-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: 2.71 Å3/Da / Density % sol: 54.55 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 24% PEG1500, 20% Glycerol, pH7.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→29 Å / Num. all: 7288 / Num. obs: 7234 / % possible obs: 99.3 % / Observed criterion σ(F): -4 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 82 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.94→3.04 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 1.9 / Num. unique all: 702 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1H65 Resolution: 2.94→25 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.911 / SU B: 32.695 / SU ML: 0.284 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 104.928 Å2
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Refine analyze | Luzzati coordinate error obs: 0.453 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.94→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.941→3.016 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 13.1466 Å / Origin y: 40.5473 Å / Origin z: 5.7409 Å
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