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Yorodumi- PDB-2r8s: High resolution structure of a specific synthetic FAB bound to P4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r8s | ||||||
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Title | High resolution structure of a specific synthetic FAB bound to P4-P6 RNA ribozyme domain | ||||||
Components |
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Keywords | IMMUNE SYSTEM/RNA / protein-RNA complex / Fab-RNA complex / IMMUNE SYSTEM-RNA COMPLEX | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / RNA / RNA (> 10) / RNA (> 100) Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Ye, J.D. / Tereshko, V. / Sidhu, S.S. / Koide, S. / Kossiakoff, A.A. / Piccirilli, J.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2008 Title: Synthetic antibodies for specific recognition and crystallization of structured RNA Authors: Ye, J.D. / Tereshko, V. / Frederiksen, J.K. / Koide, A. / Fellouse, F.A. / Sidhu, S.S. / Koide, S. / Kossiakoff, A.A. / Piccirilli, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r8s.cif.gz | 199 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r8s.ent.gz | 149.4 KB | Display | PDB format |
PDBx/mmJSON format | 2r8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2r8s_validation.pdf.gz | 466.6 KB | Display | wwPDB validaton report |
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Full document | 2r8s_full_validation.pdf.gz | 476.4 KB | Display | |
Data in XML | 2r8s_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 2r8s_validation.cif.gz | 43 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/2r8s ftp://data.pdbj.org/pub/pdb/validation_reports/r8/2r8s | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | This entry contain one asymmetric unit composed of Fab light and heavy chains L and H and RNA chain R. |
-Components
#1: RNA chain | Mass: 51420.559 Da / Num. of mol.: 1 / Mutation: Delta C209 / Source method: obtained synthetically Details: sequence occurs naturally in Tetrahymena thermophila; synthesized by in vitro transcription References: GenBank: 10840 | ||
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#2: Antibody | Mass: 23273.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: FAB SELECTION WAS DONE USING A REDUCED CODON FAB LIBRARY DISPLAYED ON THE M13 PHAGE Source: (natural) Mus musculus (house mouse) | ||
#3: Antibody | Mass: 23663.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: FAB SELECTION WAS DONE USING A REDUCED CODON FAB LIBRARY DISPLAYED ON THE M13 PHAGE Source: (natural) Mus musculus (house mouse) | ||
#4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.16 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: 34% MPD, 0.1M sodium citrate, 0.2M ammonium acetate, 25 mM magnesium chloride, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
Reflection | Resolution: 1.95→20 Å / Num. all: 77127 / Num. obs: 77127 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 16.7 | ||||||||||||||||||||
Reflection shell | Resolution: 1.95→2 Å / % possible obs: 95.5 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TZI 1HR2 Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.147 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.157 / ESU R Free: 0.141 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.918 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 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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