+Open data
-Basic information
Entry | Database: PDB / ID: 4gcw | ||||||
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Title | Crystal structure of RNase Z in complex with precursor tRNA(Thr) | ||||||
Components |
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Keywords | HYDROLASE/RNA / ZINC-DEPENDENT METALO BETALACTAMASE - RNA COMPLEX / TRNA MATURASE / PROTEIN-RNA COMPLEX / TRNA BINDING / HYDROLASE-RNA complex | ||||||
Function / homology | Function and homology information tRNase Z / 3'-tRNA processing endoribonuclease activity / zinc ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Pellegrini, O. / Li de la Sierra-Gallay, I. / Piton, J. / Gilet, L. / Condon, C. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Activation of tRNA Maturation by Downstream Uracil Residues in B. subtilis Authors: Pellegrini, O. / Li de la Sierra-Gallay, I. / Piton, J. / Gilet, L. / Condon, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gcw.cif.gz | 107.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gcw.ent.gz | 78.8 KB | Display | PDB format |
PDBx/mmJSON format | 4gcw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gc/4gcw ftp://data.pdbj.org/pub/pdb/validation_reports/gc/4gcw | HTTPS FTP |
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-Related structure data
Related structure data | 2fk6S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 35632.594 Da / Num. of mol.: 1 / Mutation: I46M, L228M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Strain: 168 / Gene: BSU23840, rnz, yqjK / Plasmid: pet21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P54548, tRNase Z | ||||
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#2: RNA chain | Mass: 24597.713 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: B.SUBTILIS TRNATHR(ENCODED BY THE TRN1-THR GENE) WAS SYNTHETISED AS A PRECURSOR WITH 2 NT 3'-EXTENSION. THE NT 73-76 ARE 2'-O-METHYLATED. | ||||
#3: Chemical | #4: Chemical | ChemComp-MES / | #5: 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: 2.75 Å3/Da / Density % sol: 55.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 28% PEG MME 2K, 0.1 M Na-MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2010 Details: KIRK PATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL |
Radiation | Monochromator: CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→43.31 Å / Num. all: 13696 / Num. obs: 13408 / % possible obs: 97.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 66.05 Å2 / Rsym value: 0.11 / Net I/σ(I): 10.71 |
Reflection shell | Resolution: 2.98→3.16 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.06 / Rsym value: 0.716 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FK6 Resolution: 3→43.3 Å / Cor.coef. Fo:Fc: 0.845 / Cor.coef. Fo:Fc free: 0.8385 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 82.7 Å2
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Refine analyze | Luzzati coordinate error obs: 0.476 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→43.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.24 Å / Total num. of bins used: 7
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