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Yorodumi- PDB-1dj0: THE CRYSTAL STRUCTURE OF E. COLI PSEUDOURIDINE SYNTHASE I AT 1.5 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dj0 | ||||||
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Title | THE CRYSTAL STRUCTURE OF E. COLI PSEUDOURIDINE SYNTHASE I AT 1.5 ANGSTROM RESOLUTION | ||||||
Components | PSEUDOURIDINE SYNTHASE I | ||||||
Keywords | LYASE / ALPHA/BETA FOLD / RNA-BINDING MOTIF / RNA-MODIFYING ENZYME | ||||||
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 (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å | ||||||
Authors | Foster, P.G. / Huang, L. / Santi, D.V. / Stroud, R.M. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 Title: The structural basis for tRNA recognition and pseudouridine formation by pseudouridine synthase I. Authors: Foster, P.G. / Huang, L. / Santi, D.V. / 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 | 1dj0.cif.gz | 232.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dj0.ent.gz | 187 KB | Display | PDB format |
PDBx/mmJSON format | 1dj0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dj0_validation.pdf.gz | 372.3 KB | Display | wwPDB validaton report |
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Full document | 1dj0_full_validation.pdf.gz | 386.2 KB | Display | |
Data in XML | 1dj0_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 1dj0_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/1dj0 ftp://data.pdbj.org/pub/pdb/validation_reports/dj/1dj0 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29723.869 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P07649, pseudouridylate synthase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.96 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: microdialysis / pH: 6.5 Details: MES BUFFER, pH 6.5, MICRODIALYSIS, temperature 298K | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 33 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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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 |
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Reflection | Resolution: 1.5→38 Å / Num. all: 83465 / Num. obs: 79453 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.07 % / Biso Wilson estimate: 17.88 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.8 | ||||||||||||||||||
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.43 % / Rmerge(I) obs: 0.35 / % possible all: 92.3 | ||||||||||||||||||
Reflection | *PLUS Num. measured all: 244026 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 92.3 % |
-Processing
Software |
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Refinement | Resolution: 1.5→38 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: USED WEIGHTED FULL MATRIX LEAST SQUARES PROCEDURE
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Refinement step | Cycle: LAST / Resolution: 1.5→38 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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