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Yorodumi- PDB-6edk: Crystal structure of the formyltransferase PseJ from Anoxybacillu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6edk | ||||||
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Title | Crystal structure of the formyltransferase PseJ from Anoxybacillus kamchatkensis with N10-formyltetrahydrofolate | ||||||
Components | Formyltransferase PseJ | ||||||
Keywords | TRANSFERASE / formyltransferase | ||||||
Function / homology | Chem-1YA Function and homology information | ||||||
Biological species | Anoxybacillus kamchatkensis G10 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Reimer, J.M. / Harb, I. / Schmeing, T.M. | ||||||
Funding support | Canada, 1items
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Citation | Journal: ACS Chem. Biol. / Year: 2018 Title: Structural Insight into a Novel Formyltransferase and Evolution to a Nonribosomal Peptide Synthetase Tailoring Domain. Authors: Reimer, J.M. / Harb, I. / Ovchinnikova, O.G. / Jiang, J. / Whitfield, C. / Schmeing, T.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6edk.cif.gz | 163.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6edk.ent.gz | 108.6 KB | Display | PDB format |
PDBx/mmJSON format | 6edk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/6edk ftp://data.pdbj.org/pub/pdb/validation_reports/ed/6edk | HTTPS FTP |
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-Related structure data
Related structure data | 6ci2SC 6ci4C 6ci5C S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 25609.049 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anoxybacillus kamchatkensis G10 (bacteria) Production host: Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-MES / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-1YA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.3 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.2M ammonium sulfate, 0.1M MES pH 6.5, 26% PEG5000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.18 Å / Num. obs: 26389 / % possible obs: 97.9 % / Redundancy: 6 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.027 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 0.763 / Num. unique obs: 1627 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6CI2 Resolution: 1.8→47.18 Å / SU ML: 0.1959 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.9222
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→47.18 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: 35.3506301031 Å / Origin y: 18.4195241171 Å / Origin z: 6.93756437028 Å
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Refinement TLS group | Selection details: all |