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Yorodumi- PDB-2j3l: Prolyl-tRNA synthetase from Enterococcus faecalis complexed with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2j3l | ||||||
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Title | Prolyl-tRNA synthetase from Enterococcus faecalis complexed with a prolyl-adenylate analogue ('5'-O-(N-(L-PROLYL)-SULFAMOYL)ADENOSINE) | ||||||
Components | PROLYL-TRNA SYNTHETASE | ||||||
Keywords | LIGASE / BACTERIAL-TYPE PROLYL-TRNA SYNTHETASE / CLASS II AMINOACYL- TRNA SYNTHETASE / EDITING / TRANSLATION / ATP + L-PROLINE + TRNA (PRO) GIVES AMP + PPI + L-PROLYL-TRNA(PRO) | ||||||
Function / homology | Function and homology information proline-tRNA ligase / proline-tRNA ligase activity / prolyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / transferase activity / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ENTEROCOCCUS FAECALIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Crepin, T. / Yaremchuk, A. / Tukalo, M. / Cusack, S. | ||||||
Citation | Journal: Structure / Year: 2006 Title: Structures of Two Bacterial Prolyl-tRNA Synthetases with and without a Cis-Editing Domain. Authors: Crepin, T. / Yaremchuk, A. / Tukalo, M. / Cusack, S. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j3l.cif.gz | 237.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j3l.ent.gz | 191.1 KB | Display | PDB format |
PDBx/mmJSON format | 2j3l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2j3l_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2j3l_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2j3l_validation.xml.gz | 42.9 KB | Display | |
Data in CIF | 2j3l_validation.cif.gz | 59.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/2j3l ftp://data.pdbj.org/pub/pdb/validation_reports/j3/2j3l | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.680755, 0.716749, -0.15114), Vector: |
-Components
#1: Protein | Mass: 64341.555 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ENTEROCOCCUS FAECALIS (bacteria) / Plasmid: PQE-60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: Q831W7, proline-tRNA ligase #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: 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: 2.56 Å3/Da / Density % sol: 52 % Description: MAP IMPROVED BY RESOLVE USING PRIME AND SWITCH MODE AND 2-FOLD NCS |
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Crystal grow | Details: 52% AMMONIUM SULPHATE, PROLYL-ADENYLATE ANALOGUE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 28, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 58612 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.3→2.4 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.4 / % possible all: 82.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PRORS FROM RHODOPSEUDOMONAS PALUSTRIS Resolution: 2.3→100.5 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.894 / SU B: 15.246 / SU ML: 0.189 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.336 / ESU R Free: 0.255 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→100.5 Å
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Refine LS restraints |
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