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Yorodumi- PDB-6abm: Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6abm | ||||||
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Title | Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with pTmdZLys | ||||||
Components | Pyrrolysine--tRNA ligase | ||||||
Keywords | TRANSLATION / aminoacyl-tRNA synthetase / non-natural amino acids / pyrrolysyl-tRNA synthetase / tRNA | ||||||
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: 1.368 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 | 6abm.cif.gz | 150.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6abm.ent.gz | 114.4 KB | Display | PDB format |
PDBx/mmJSON format | 6abm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6abm_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6abm_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6abm_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 6abm_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/6abm ftp://data.pdbj.org/pub/pdb/validation_reports/ab/6abm | HTTPS FTP |
-Related structure data
Related structure data | 6aacC 6aadC 6aanC 6aaoC 6aapC 6aaqC 6aazC 6ab0C 6ab1C 6ab2C 6ab8C 6abkC 6ablC 2zceS 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, 333 molecules
#2: Chemical | #3: Chemical | ChemComp-ATP / | #4: Chemical | ChemComp-9VR / ( | #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: 2.29 Å3/Da / Density % sol: 46.22 % |
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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: BL32XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.368→50 Å / Num. obs: 59383 / % possible obs: 99.6 % / Redundancy: 4.7 % / Rpim(I) all: 0.075 / Rrim(I) all: 0.166 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.37→1.4 Å / Num. unique obs: 2804 / Rpim(I) all: 0.304 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2zim, 2zce Resolution: 1.368→35.024 Å / SU ML: 0.14 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 19.85 / 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: 1.368→35.024 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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