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Yorodumi- PDB-4m9q: Crystal structure of C-terminally truncated Arl13B from Chlamydom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m9q | ||||||
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Title | Crystal structure of C-terminally truncated Arl13B from Chlamydomonas rheinhardtii bound to GppNHp | ||||||
Components | ARF-like GTPase | ||||||
Keywords | HYDROLASE / GTPase / G domain / Joubert Syndrome / cilia | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Miertzschke, M. / Koerner, C. / Spoerner, M. / Wittinghofer, A. | ||||||
Citation | Journal: Biochem.J. / Year: 2014 Title: Structural insights into the small G-protein Arl13B and implications for Joubert syndrome. Authors: Miertzschke, M. / Koerner, C. / Spoerner, M. / Wittinghofer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m9q.cif.gz | 263.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m9q.ent.gz | 212.2 KB | Display | PDB format |
PDBx/mmJSON format | 4m9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m9/4m9q ftp://data.pdbj.org/pub/pdb/validation_reports/m9/4m9q | HTTPS FTP |
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-Related structure data
Related structure data | 1kshS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 25852.311 Da / Num. of mol.: 3 / Fragment: UNP residues 18-242 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: ARL13, CHLREDRAFT_195529 / Production host: Escherichia coli (E. coli) / References: UniProt: A8INQ0, small monomeric GTPase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.22 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M ammonium sulfate, 0.1 M MES, pH 6.5, 30% PEG5000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.99 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2012 |
Radiation | Monochromator: silicon mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→19.83 Å / Num. all: 22958 / Num. obs: 22891 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 14.4 % / Rsym value: 0.065 / Net I/σ(I): 30.03 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 14.7 % / Mean I/σ(I) obs: 5.78 / Rsym value: 0.519 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KSH Resolution: 2.5→19.83 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 18.783 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.746 / ESU R Free: 0.285 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.618 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→19.83 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.6 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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