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Yorodumi- PDB-3vqy: Crystal structure of the catalytic domain of pyrrolysyl-tRNA synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vqy | ||||||
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Title | Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in complex with BocLys and AMPPNP (form 2) | ||||||
Components | Pyrrolysine--tRNA ligase | ||||||
Keywords | LIGASE / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / aminoacyl-tRNA synthetase / pyrrolysyl-tRNA synthetase / AMPPNP / BocLys | ||||||
Function / homology | Function and homology information Helix hairpin bin / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Methanosarcina mazei (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Yanagisawa, T. / Sumida, T. / Ishii, R. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site Authors: Yanagisawa, T. / Sumida, T. / Ishii, R. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vqy.cif.gz | 72.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vqy.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 3vqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vqy_validation.pdf.gz | 934.3 KB | Display | wwPDB validaton report |
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Full document | 3vqy_full_validation.pdf.gz | 941.2 KB | Display | |
Data in XML | 3vqy_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 3vqy_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/3vqy ftp://data.pdbj.org/pub/pdb/validation_reports/vq/3vqy | HTTPS FTP |
-Related structure data
Related structure data | 3vqvC 3vqwSC 3vqxC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33344.164 Da / Num. of mol.: 1 / Mutation: E444G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: JCM9314 / Gene: pylS / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: pyrrolysine-tRNAPyl ligase | ||||
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#2: Chemical | ChemComp-ANP / | ||||
#3: Chemical | ChemComp-LBY / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS STRAIN OF SOURCE (METHANOSARCINA MAZEI JCM9314) DOES NOT ...A SEQUENCE DATABASE REFERENCE FOR THIS STRAIN OF SOURCE (METHANOSAR | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Na/Cacodylate, MgCl2, PEG3350, pH 7.0, 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: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 16, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 16537 / % possible obs: 97.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 36.9 Å2 / Rsym value: 0.079 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 3.4 % / Rsym value: 0.247 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VQW Resolution: 2.4→41.76 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1356310.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.5657 Å2 / ksol: 0.346821 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→41.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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