+Open data
-Basic information
Entry | Database: PDB / ID: 3h3a | ||||||
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Title | The complex structure of CCA-adding enzyme with CTP | ||||||
Components | TRNA nucleotidyl transferase-related protein | ||||||
Keywords | TRANSFERASE / TRANSFERASE/RNA / Nucleotide-binding / Nucleotidyltransferase / RNA-binding | ||||||
Function / homology | Function and homology information RNA 3'-end processing / nucleotidyltransferase activity / tRNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.801 Å | ||||||
Authors | Toh, Y. / Tomita, K. | ||||||
Citation | Journal: Embo J. / Year: 2009 Title: Mechanism for the definition of elongation and termination by the class II CCA-adding enzyme Authors: Toh, Y. / Takeshita, D. / Numata, T. / Fukai, S. / Nureki, O. / Tomita, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h3a.cif.gz | 358.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h3a.ent.gz | 298 KB | Display | PDB format |
PDBx/mmJSON format | 3h3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h3a_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3h3a_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3h3a_validation.xml.gz | 38.2 KB | Display | |
Data in CIF | 3h3a_validation.cif.gz | 51.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h3/3h3a ftp://data.pdbj.org/pub/pdb/validation_reports/h3/3h3a | HTTPS FTP |
-Related structure data
Related structure data | 3h37SC 3h38C 3h39C 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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Unit cell |
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-Components
#1: Protein | Mass: 51530.617 Da / Num. of mol.: 2 / Fragment: UNP residues 437-863 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WZH4, EC: 2.7.7.25 #2: Chemical | #3: 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: 4.36 Å3/Da / Density % sol: 71.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4 Details: 20% ethylene glycol, 0.05M Tris-Cl pH8.4, 2mM CTP, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2007 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 42184 / % possible obs: 95.5 % / Redundancy: 3 % / Biso Wilson estimate: 86.23 Å2 / Rsym value: 0.039 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 3778 / Rsym value: 0.369 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3H37 Resolution: 2.801→31.793 Å / SU ML: 0.7 / Cross valid method: THROUGHOUT / σ(F): 1.45 / 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 / Bsol: 82.9 Å2 / ksol: 0.293 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.801→31.793 Å
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Refine LS restraints |
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LS refinement shell |
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