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Yorodumi- PDB-2nre: Crystal structure of pseudoudirinde synthase TruA in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nre | ||||||
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Title | Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA | ||||||
Components |
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Keywords | ISOMERASE/RNA / pseudouridine synthase / anticodon stem loop / tRNA / multisite specificity / ISOMERASE-RNA COMPLEX | ||||||
Function / homology | Function and homology information tRNA pseudouridine(38-40) synthase activity / tRNA pseudouridine38-40 synthase / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å | ||||||
Authors | Hur, S. / Stroud, R.M. | ||||||
Citation | Journal: Mol.Cell / Year: 2007 Title: How U38, 39, and 40 of Many tRNAs Become the Targets for Pseudouridylation by TruA. Authors: Hur, S. / Stroud, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nre.cif.gz | 127.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nre.ent.gz | 96.5 KB | Display | PDB format |
PDBx/mmJSON format | 2nre.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nre_validation.pdf.gz | 454.9 KB | Display | wwPDB validaton report |
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Full document | 2nre_full_validation.pdf.gz | 485 KB | Display | |
Data in XML | 2nre_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 2nre_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/2nre ftp://data.pdbj.org/pub/pdb/validation_reports/nr/2nre | HTTPS FTP |
-Related structure data
Related structure data | 2nqpC 2nr0C 1dj0S 1ehzS 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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Unit cell |
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Details | A molecule of id A forms a dimer with its crystallographic symmetry mate (y,x,-z), and F is the substrate tRNA bound to the enzyme. |
-Components
#1: RNA chain | Mass: 28094.645 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Occurs naturally in E. coli. Synthesized by T7 in vitro transcription |
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#2: Protein | Mass: 30441.615 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: truA / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 References: UniProt: P07649, tRNA pseudouridine38-40 synthase |
#3: Chemical |
-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: 65.13 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20% PEG 3350, 0.2 M K3 Citrate, 5 mM spermine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 9, 2004 |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 4→20 Å / Num. all: 6998 / Num. obs: 6998 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rsym value: 0.172 / Net I/σ(I): 9.53 |
Reflection shell | Resolution: 4→4.14 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3.38 / Num. unique all: 664 / Rsym value: 0.531 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DJ0 and 1EHZ Resolution: 4→20 Å / Cor.coef. Fo:Fc: 0.842 / Cor.coef. Fo:Fc free: 0.708 / SU B: 71.759 / SU ML: 0.98 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 1.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS TLS parameter was refined for tRNA (treated as a single TLS group)
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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: 63.983 Å2
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Refinement step | Cycle: LAST / Resolution: 4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4→4.1 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -13.558 Å / Origin y: -28.623 Å / Origin z: 25.55 Å
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