[English] 日本語
Yorodumi- PDB-1jsx: Crystal Structure of the Escherichia coli Glucose-Inhibited Divis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jsx | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Escherichia coli Glucose-Inhibited Division Protein B (GidB) | ||||||
Components | Glucose-inhibited division protein B | ||||||
Keywords | UNKNOWN FUNCTION / methyltransferase fold / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information 16S rRNA (guanine527-N7)-methyltransferase / rRNA (guanine-N7-)-methyltransferase activity / rRNA base methylation / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Romanowski, M.J. / Bonanno, J.B. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Proteins / Year: 2002 Title: Crystal structure of the Escherichia coli glucose-inhibited division protein B (GidB) reveals a methyltransferase fold. Authors: Romanowski, M.J. / Bonanno, J.B. / Burley, S.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1jsx.cif.gz | 52.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1jsx.ent.gz | 37.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jsx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jsx_validation.pdf.gz | 421.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1jsx_full_validation.pdf.gz | 427.7 KB | Display | |
Data in XML | 1jsx_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 1jsx_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/1jsx ftp://data.pdbj.org/pub/pdb/validation_reports/js/1jsx | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23461.102 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: gidB / Plasmid: pGEX6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A6U5 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.23 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 15% PEG4000, 10% isopropanol, 0.1M sodium citrate pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| ||||||||||||||||||
Detector |
| ||||||||||||||||||
Radiation |
| ||||||||||||||||||
Radiation wavelength |
| ||||||||||||||||||
Reflection | Resolution: 2.4→30 Å / Num. all: 9170 / Num. obs: 9170 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 27.6 Å2 / Rsym value: 0.078 | ||||||||||||||||||
Reflection shell | Resolution: 2.4→2.55 Å / % possible all: 98.1 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 30 Å |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.4→17.97 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 663404.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.6735 Å2 / ksol: 0.375812 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.1 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→17.97 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 18 Å / Rfactor obs: 0.24 / Rfactor Rfree: 0.275 / Rfactor Rwork: 0.24 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.329 / Rfactor Rwork: 0.231 / Rfactor obs: 0.231 |