[English] 日本語
Yorodumi- PDB-1xxl: The crystal structure of YcgJ protein from Bacillus subitilis at ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xxl | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of YcgJ protein from Bacillus subitilis at 2.1 A resolution | ||||||
Components | YcgJ protein | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein Structure Initiative / PSI / New York SGX Research Center for Structural Genomics / NYSGXRC / probable methyltransferase | ||||||
Function / homology | Function and homology information S-adenosylmethionine-dependent methyltransferase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Burke, T.A. / Gorman, J. / Shaprio, L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: The crystal structure of YcgJ protein from Bacillus subitilis at 2.1 A resolution Authors: Burke, T.A. / Gorman, J. / Shapiro, L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1xxl.cif.gz | 109.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1xxl.ent.gz | 88.9 KB | Display | PDB format |
PDBx/mmJSON format | 1xxl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xxl_validation.pdf.gz | 451.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1xxl_full_validation.pdf.gz | 454.1 KB | Display | |
Data in XML | 1xxl_validation.xml.gz | 22 KB | Display | |
Data in CIF | 1xxl_validation.cif.gz | 32.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/1xxl ftp://data.pdbj.org/pub/pdb/validation_reports/xx/1xxl | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 27263.064 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: YcgJ / Plasmid: modified pET 28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Bl21 / References: UniProt: O31474 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.11 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.4M Am Sulfate, 0.1M Na Citrate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 9, 2004 Details: Diamond monochromator and horizontal, vertical focusing mirrors |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 37699 / Num. obs: 37661 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.43 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 16.66 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 6.75 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 9.35 / Num. unique all: 3711 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / SU B: 4.16 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.173 / ESU R Free: 0.162 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.301 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.102→2.156 Å / Total num. of bins used: 20
|