+Open data
-Basic information
Entry | Database: PDB / ID: 3cnl | ||||||
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Title | Crystal structure of GNP-bound YlqF from T. maritima | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | SIGNALING PROTEIN / YlqF / circular permutation / GNP | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å | ||||||
Authors | Kim, D.J. / Jang, J.Y. / Yoon, H.-J. / Suh, S.W. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal structure of YlqF, a circularly permuted GTPase: Implications for its GTPase activation in 50 S ribosomal subunit assembly Authors: Kim, D.J. / Jang, J.Y. / Yoon, H.-J. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cnl.cif.gz | 109.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cnl.ent.gz | 84.3 KB | Display | PDB format |
PDBx/mmJSON format | 3cnl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/3cnl ftp://data.pdbj.org/pub/pdb/validation_reports/cn/3cnl | HTTPS FTP |
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-Related 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: 29642.502 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0768 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZM6 |
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#2: Chemical | ChemComp-GNP / |
#3: 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: 2.34 Å3/Da / Density % sol: 47.35 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM HEPES (pH 7.5), 5% (v/v) isopropanol, 20% (w/v) polyethylene glycol 4000, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23985 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23985 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 19460 |
Reflection shell | Resolution: 2→2.07 Å / Num. unique all: 19460 |
-Processing
Software |
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Refinement | Resolution: 2→19.01 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 10.822 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R Free: 0.202 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.761 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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