+Open data
-Basic information
Entry | Database: PDB / ID: 3cno | ||||||
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Title | GDP-bound structue of TM YlqF | ||||||
Components | Putative uncharacterized protein | ||||||
Keywords | SIGNALING PROTEIN / YlqF / circular permutation / GDP | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 | 3cno.cif.gz | 62 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cno.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 3cno.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/3cno ftp://data.pdbj.org/pub/pdb/validation_reports/cn/3cno | HTTPS FTP |
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-Related structure data
Related structure data | 3cnlC 3cnnC 1pujS 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: 29642.502 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0768 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZM6 |
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#2: Chemical | ChemComp-GDP / |
#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: 2.32 Å3/Da / Density % sol: 47 % |
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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 / Date: Sep 23, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23985 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 12683 / Num. obs: 12683 |
Reflection shell | Resolution: 2.3→2.38 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PUJ Resolution: 2.3→19.07 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.105 / SU ML: 0.217 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.382 / ESU R Free: 0.274 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.998 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→19.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.304→2.362 Å / Total num. of bins used: 20
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