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Yorodumi- PDB-3g9c: Crystal structure of the product Bacillus anthracis glmS ribozyme -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g9c | ||||||
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Title | Crystal structure of the product Bacillus anthracis glmS ribozyme | ||||||
Components |
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Keywords | RNA binding protein/RNA / catalytic RNA / Acetylation / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / Ribonucleoprotein / RNA-binding / Spliceosome / RNA binding protein-RNA complex | ||||||
Function / homology | Function and homology information U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm ...U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) syntetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å | ||||||
Authors | Strobel, S.A. / Cochrane, J.C. / Lipchock, S.V. / Smith, K.D. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme Authors: Cochrane, J.C. / Lipchock, S.V. / Smith, K.D. / Strobel, S.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g9c.cif.gz | 383 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g9c.ent.gz | 312.9 KB | Display | PDB format |
PDBx/mmJSON format | 3g9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g9c_validation.pdf.gz | 782.1 KB | Display | wwPDB validaton report |
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Full document | 3g9c_full_validation.pdf.gz | 818.7 KB | Display | |
Data in XML | 3g9c_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 3g9c_validation.cif.gz | 48.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/3g9c ftp://data.pdbj.org/pub/pdb/validation_reports/g9/3g9c | HTTPS FTP |
-Related 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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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 4
NCS ensembles :
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-Components
-RNA chain , 2 types, 8 molecules EFGHPQRS
#2: RNA chain | Mass: 3505.170 Da / Num. of mol.: 4 / Mutation: 2'-OH at A-1 / Source method: obtained synthetically / Details: synthesized at Dharmacon / Source: (synth.) syntetic construct (others) #3: RNA chain | Mass: 45624.859 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: in vitro transcribed from a DNA template / Source: (synth.) syntetic construct (others) |
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-Protein / Sugars , 2 types, 5 molecules ABCD
#1: Protein | Mass: 11340.315 Da / Num. of mol.: 4 / Fragment: RNA BINDING DOMAIN / Mutation: Y31H,Q36R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P09012 #4: Sugar | ChemComp-GLP / | |
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-Non-polymers , 2 types, 24 molecules
#5: Chemical | #6: 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: 2.44 Å3/Da / Density % sol: 49.49 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 59605 / % possible obs: 95.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.138 / Χ2: 1.069 / Net I/σ(I): 13.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 2.9→49.69 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.861 / Occupancy max: 1 / Occupancy min: 1 / SU B: 52.341 / SU ML: 0.459 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.525 / 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 max: 86.99 Å2 / Biso mean: 35.364 Å2 / Biso min: 11.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→49.69 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
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