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Yorodumi- PDB-4cs1: Crystal structure of a simple duplex kink turn, HmKt-7 with 2 Mg ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cs1 | ||||||||||||||||||||
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Title | Crystal structure of a simple duplex kink turn, HmKt-7 with 2 Mg bound. | ||||||||||||||||||||
Components | 5'-(*Keywords | RNA / KINK TURN / METAL ION | Function / homology | RNA / RNA (> 10) | Function and homology information Biological species | HALOARCULA MARISMORTUI (Halophile) | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | Authors | Huang, L. / Lilley, D.M.J. | Citation | Journal: Nat.Commun. / Year: 2014 | Title: A Critical Base Pair in K-Turns that Confers Folding Characteristics and Correlates with Biological Function. Authors: Mcphee, S.A. / Huang, L. / Lilley, D.M.J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cs1.cif.gz | 33.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cs1.ent.gz | 23.6 KB | Display | PDB format |
PDBx/mmJSON format | 4cs1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/4cs1 ftp://data.pdbj.org/pub/pdb/validation_reports/cs/4cs1 | HTTPS FTP |
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-Related structure data
Related structure data | 4c40S 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 on special symmetry positions |
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-Components
#1: RNA chain | Mass: 6233.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HALOARCULA MARISMORTUI (Halophile) | ||
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#2: Chemical | #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: 2.53 Å3/Da / Density % sol: 51.44 % / Description: NONE |
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Crystal grow | pH: 4 / Details: 3.5 M SODIUM FORMATE, 0.1 M SODIUM ACETATE PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2→37.4 Å / Num. obs: 4920 / % possible obs: 98.4 % / Observed criterion σ(I): 1.4 / Redundancy: 6.3 % / Biso Wilson estimate: 42.78 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.33 / Mean I/σ(I) obs: 1.4 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4C40 Resolution: 2→37.415 Å / SU ML: 0.21 / σ(F): 1.35 / Phase error: 25.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→37.415 Å
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Refine LS restraints |
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LS refinement shell |
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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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