[English] 日本語
Yorodumi- PDB-5th5: Crystal Structure of QueE from Bacillus subtilis with 6-carboxypt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5th5 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of QueE from Bacillus subtilis with 6-carboxypterin-5'-deoxyadenosyl ester bound | |||||||||
Components | 7-carboxy-7-deazaguanine synthase | |||||||||
Keywords | LYASE / S-Adenosylmethionine radical enzyme / 7-Carboxy-7-deazaguanine synthase | |||||||||
Function / homology | Function and homology information 7-carboxy-7-deazaguanine synthase / carbon-nitrogen lyase activity / queuosine biosynthetic process / S-adenosyl-L-methionine binding / 4 iron, 4 sulfur cluster binding / magnesium ion binding / protein homodimerization activity Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.407 Å | |||||||||
Authors | Grell, T.A.J. / Dowling, D.P. / Drennan, C.L. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: J. Am. Chem. Soc. / Year: 2017 Title: 7-Carboxy-7-deazaguanine Synthase: A Radical S-Adenosyl-l-methionine Enzyme with Polar Tendencies. Authors: Bruender, N.A. / Grell, T.A. / Dowling, D.P. / McCarty, R.M. / Drennan, C.L. / Bandarian, V. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5th5.cif.gz | 209.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5th5.ent.gz | 166 KB | Display | PDB format |
PDBx/mmJSON format | 5th5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5th5_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5th5_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5th5_validation.xml.gz | 39.6 KB | Display | |
Data in CIF | 5th5_validation.cif.gz | 50.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/5th5 ftp://data.pdbj.org/pub/pdb/validation_reports/th/5th5 | HTTPS FTP |
-Related structure data
Related structure data | 5tgsSC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
|
-Components
#1: Protein | Mass: 29323.311 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: queE, ykvL, BSU13740 / Production host: Escherichia coli (E. coli) References: UniProt: O31677, 7-carboxy-7-deazaguanine synthase #2: Chemical | ChemComp-SF4 / #3: Chemical | ChemComp-7C5 / #4: Chemical | ChemComp-MET / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.66 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 1 M trisodium citrate (pH 4.2), 1.5 M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.407→44.504 Å / Num. obs: 40846 / % possible obs: 98.8 % / Redundancy: 3.2 % / Rsym value: 0.099 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.407→2.46 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.1 / % possible all: 93.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TGS Resolution: 2.407→44.504 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.95
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.407→44.504 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|