+Open data
-Basic information
Entry | Database: PDB / ID: 3oxm | ||||||
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Title | crystal structure of glycine riboswitch, Tl-Acetate soaked | ||||||
Components | (domain II of glycine ...) x 2 | ||||||
Keywords | RNA / Gene expression regulator / glycine riboswitch | ||||||
Function / homology | GLYCINE / THALLIUM (I) ION / : / RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Huang, L. / Serganov, A. / Patel, D.J. | ||||||
Citation | Journal: Mol.Cell / Year: 2010 Title: Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch. Authors: Huang, L. / Serganov, A. / Patel, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3oxm.cif.gz | 207 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3oxm.ent.gz | 164.6 KB | Display | PDB format |
PDBx/mmJSON format | 3oxm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3oxm_validation.pdf.gz | 436.9 KB | Display | wwPDB validaton report |
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Full document | 3oxm_full_validation.pdf.gz | 440.5 KB | Display | |
Data in XML | 3oxm_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 3oxm_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ox/3oxm ftp://data.pdbj.org/pub/pdb/validation_reports/ox/3oxm | HTTPS FTP |
-Related structure data
Related structure data | 3owiSC 3owwC 3owzC 3ox0C 3oxbC 3oxdC 3oxeC 3oxjC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Domain II of glycine ... , 2 types, 2 molecules AB
#1: RNA chain | Mass: 28735.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcription / References: GenBank: CP001485.1 |
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#2: RNA chain | Mass: 28655.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcription / References: GenBank: CP001485.1 |
-Non-polymers , 4 types, 75 molecules
#3: Chemical | #4: Chemical | ChemComp-TL / #5: Chemical | ChemComp-MG / #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | THE ORIGINAL MG AND TL CHAIN IDS HAVE BEEN CHANGED TO THE CLOSEST POLYMER CHAIN. 100 HAS BEEN ADDED ...THE ORIGINAL MG AND TL CHAIN IDS HAVE BEEN CHANGED TO THE CLOSEST POLYMER CHAIN. 100 HAS BEEN ADDED TO THE ORIGINAL MG and 200 HAS BEEN ADDED TO THE ORIGINAL TL RESIDUE NUMBERS. |
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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: 3.53 Å3/Da / Density % sol: 65.18 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.1 Details: 0.05 M Na-cacodylate, pH 5.1, 0.2 M KCl, 8 % (w/v) PEG8000 and 80 mM magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9763 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2009 |
Radiation | Monochromator: SI mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→20 Å / Num. all: 17793 / Num. obs: 17793 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 47.7 |
Reflection shell | Resolution: 2.95→3 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.51 / Num. unique all: 881 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3OWI Resolution: 2.95→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.937 / SU B: 28.527 / SU ML: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.325 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.95→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.025 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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