[English] 日本語
Yorodumi- PDB-6ci4: Crystal structure of the formyltransferase PseJ from Anoxybacillu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ci4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the formyltransferase PseJ from Anoxybacillus kamchatkensis soaked with UDP-4-amino-4,6-dideoxy-L-AltNAc | ||||||
Components | formyltransferase PseJ | ||||||
Keywords | TRANSFERASE / formyltransferase | ||||||
Function / homology | Chem-F5P Function and homology information | ||||||
Biological species | Anoxybacillus kamchatkensis G10 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82406793237 Å | ||||||
Authors | Harb, I. / Reimer, J.M. / Schmeing, T.M. | ||||||
Funding support | Canada, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ci4.cif.gz | 158.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ci4.ent.gz | 105.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ci4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ci4_validation.pdf.gz | 794.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ci4_full_validation.pdf.gz | 795.7 KB | Display | |
Data in XML | 6ci4_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 6ci4_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/6ci4 ftp://data.pdbj.org/pub/pdb/validation_reports/ci/6ci4 | HTTPS FTP |
-Related structure data
Related structure data | 6ci2SC 6ci5C 6edkC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-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) |
---|---|
#2: Chemical | ChemComp-F5P / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.44 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M ammonium sulfate, 0.1 M MES pH 6.5, 28.4% PEG5000 MME |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 12, 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: 1.82→46.89 Å / Num. obs: 23891 / % possible obs: 93.9 % / Redundancy: 2.8 % / Biso Wilson estimate: 33.9361522933 Å2 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.82→1.85 Å / Num. unique obs: 1025 / CC1/2: 0.691 / Rpim(I) all: 0.398 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6CI2 Resolution: 1.82406793237→46.8854873102 Å / SU ML: 0.243767715036 / Cross valid method: FREE R-VALUE / σ(F): 1.37584249725 / Phase error: 24.4032592997
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.5865318402 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82406793237→46.8854873102 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 35.0366418687 Å / Origin y: 20.2339551917 Å / Origin z: 7.16782828339 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |