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Yorodumi- PDB-6aad: Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6aad | ||||||
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Title | Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with mTmdZLys | ||||||
Components | Pyrrolysine--tRNA ligase | ||||||
Keywords | TRANSLATION / aminoacyl-tRNA synthetase / non-natural amino acids | ||||||
Function / homology | Function and homology information pyrrolysine-tRNAPyl ligase / pyrrolysyl-tRNA synthetase activity / tRNA aminoacylation for protein translation / tRNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Methanosarcina mazei JCM 9314 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.444 Å | ||||||
Authors | Yanagisawa, T. / Kuratani, M. / Yokoyama, S. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Cell Chem Biol / Year: 2019 Title: Structural Basis for Genetic-Code Expansion with Bulky Lysine Derivatives by an Engineered Pyrrolysyl-tRNA Synthetase. Authors: Yanagisawa, T. / Kuratani, M. / Seki, E. / Hino, N. / Sakamoto, K. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6aad.cif.gz | 145.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aad.ent.gz | 110.6 KB | Display | PDB format |
PDBx/mmJSON format | 6aad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6aad_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6aad_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6aad_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 6aad_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/6aad ftp://data.pdbj.org/pub/pdb/validation_reports/aa/6aad | HTTPS FTP |
-Related structure data
Related structure data | 6aacC 6aanC 6aaoC 6aapC 6aaqC 6aazC 6ab0C 6ab1C 6ab2C 6ab8C 6abkC 6ablC 6abmC 2zimS C: citing same article (ref.) S: Starting model for refinement |
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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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 31346.982 Da / Num. of mol.: 1 / Mutation: Y306A,Y384F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina mazei JCM 9314 (archaea) Gene: pylS / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): rosetta / References: UniProt: Q8PWY1, pyrrolysine-tRNAPyl ligase |
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-Non-polymers , 5 types, 290 molecules
#2: Chemical | #3: Chemical | ChemComp-ATP / | #4: Chemical | ChemComp-9TU / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | The sequence reference Q8PWY1 (PYLS_METMA) is derived from a different strain (Methanosarcina mazei ...The sequence reference Q8PWY1 (PYLS_METMA) is derived from a different strain (Methanosarcina mazei Go1, TaxID 192952). Residue E444G is a natural mutation observed in PylRS gene from Methanosarcina mazei JCM 9314 genome. |
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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: 2.23 Å3/Da / Density % sol: 44.96 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Tris-HCl buffer (pH 8.5),PEG 200, KCl, MgCl2, sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 28, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→50 Å / Num. obs: 48373 / % possible obs: 97.4 % / Redundancy: 7.2 % / Rpim(I) all: 0.027 / Rrim(I) all: 0.074 / Net I/σ(I): 34.2 |
Reflection shell | Resolution: 1.44→1.48 Å / Num. unique obs: 2317 / Rpim(I) all: 0.283 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZIM Resolution: 1.444→35.019 Å / SU ML: 0.13 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 18.89 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.444→35.019 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 71.548 Å / Origin y: 23.175 Å / Origin z: 27.832 Å
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Refinement TLS group | Selection details: all |