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Yorodumi- PDB-6ci5: Crystal structure of the formyltransferase PseJ from Anoxybacillu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ci5 | ||||||
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Title | Crystal structure of the formyltransferase PseJ from Anoxybacillus kamchatkensis in complex with UDP-4,6-dideoxy-4-formamido-L-AltNAc and tetrahydrofolate | ||||||
Components | formyltransferase PseJ | ||||||
Keywords | TRANSFERASE / formyltransferase | ||||||
Function / homology | Chem-1YJ / Chem-F5G Function and homology information | ||||||
Biological species | Anoxybacillus kamchatkensis G10 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.00003052726 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 | 6ci5.cif.gz | 156.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ci5.ent.gz | 105 KB | Display | PDB format |
PDBx/mmJSON format | 6ci5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ci5_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6ci5_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6ci5_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 6ci5_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/6ci5 ftp://data.pdbj.org/pub/pdb/validation_reports/ci/6ci5 | HTTPS FTP |
-Related structure data
Related structure data | 6ci2SC 6ci4C 6edkC 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-SO4 / |
#3: Chemical | ChemComp-F5G / ( |
#4: Chemical | ChemComp-1YJ / |
#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: 2.85 Å3/Da / Density % sol: 56.84 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium sulfate, 0.1 M MES pH 6.5, 25.6% PEG5000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→47.23 Å / Num. obs: 32206 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 48.8393855317 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.9→1.94 Å / Rmerge(I) obs: 0.984 / Num. unique obs: 1720 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6CI2 Resolution: 2.00003052726→46.8838402268 Å / SU ML: 0.312089467255 / Cross valid method: FREE R-VALUE / σ(F): 1.47364596753 / Phase error: 30.9228387233 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 74.0064049426 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.00003052726→46.8838402268 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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