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Yorodumi- PDB-6ahw: Crystal structure of circular-permutated YibK methyltransferase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ahw | ||||||
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Title | Crystal structure of circular-permutated YibK methyltransferase from Haemophilus influenzae | ||||||
Components | circular-permutated tRNA (cytidine(34)-2'-O)-methyltransferase | ||||||
Keywords | TRANSFERASE / methyltransferase / circular permutation | ||||||
Function / homology | Function and homology information tRNA (cytidine(34)-2'-O)-methyltransferase activity / tRNA (5-carboxymethylaminomethyluridine(34)-2'-O)-methyltransferase activity / wobble position cytosine ribose methylation / wobble position uridine ribose methylation / tRNA (cytidine34-2'-O)-methyltransferase / RNA binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Haemophilus influenzae Rd KW20 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å | ||||||
Authors | Chuang, Y.C. / Lyu, P.C. / Hsu, S.T.D. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2019 Title: Untying a Protein Knot by Circular Permutation. Authors: Chuang, Y.C. / Hu, I.C. / Lyu, P.C. / Hsu, S.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ahw.cif.gz | 149.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ahw.ent.gz | 117.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ahw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/6ahw ftp://data.pdbj.org/pub/pdb/validation_reports/ah/6ahw | HTTPS FTP |
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-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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 2 - 163 / Label seq-ID: 2 - 163
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-Components
#1: Protein | Mass: 18702.738 Da / Num. of mol.: 2 / Fragment: UNP residues 82-160,UNP residues 1-81 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae Rd KW20 (bacteria) Strain: KW20 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P44868, tRNA (cytidine34-2'-O)-methyltransferase #2: 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: 2.28 Å3/Da / Density % sol: 46.11 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% PEG8000, 0.1M sodium cacodylate, 0.2M sodium acetate, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→30 Å / Num. obs: 48195 / % possible obs: 99.6 % / Redundancy: 4 % / Biso Wilson estimate: 25.66 Å2 / Net I/σ(I): 23.47 |
Reflection shell | Resolution: 1.56→1.62 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.88 / Num. unique obs: 4806 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→29.85 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.348 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.09 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.943 Å2
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Refinement step | Cycle: 1 / Resolution: 1.56→29.85 Å
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Refine LS restraints |
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