[English] 日本語
Yorodumi- PDB-3m33: The crystal structure of a functionally unknown protein from Dein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m33 | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of a functionally unknown protein from Deinococcus radiodurans R1 | ||||||
Components | Uncharacterized protein | ||||||
Keywords | Structural Genomics / Unknown function / PSI-2 / protein structure initiative / MCSG / Midwest Center for Structural Genomics | ||||||
Function / homology | Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.195 Å | ||||||
Authors | Tan, K. / Mack, J. / Feldmann, B. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a functionally unknown protein from Deinococcus radiodurans R1 Authors: Tan, K. / Mack, J. / Feldmann, B. / Joachimiak, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3m33.cif.gz | 178.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3m33.ent.gz | 149.4 KB | Display | PDB format |
PDBx/mmJSON format | 3m33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/3m33 ftp://data.pdbj.org/pub/pdb/validation_reports/m3/3m33 | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25317.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Strain: R1 / Gene: DR_0468 / Plasmid: pMCSG19b / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q9RX47 #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.66 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M HEPES, 1.26M (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97911, 0.97962 | |||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 7, 2010 / Details: mirror | |||||||||
Radiation | Monochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 2.2→35 Å / Num. all: 38704 / Num. obs: 38704 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 42.4 | |||||||||
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 3.25 / Num. unique all: 1940 / Rsym value: 0.194 / % possible all: 96 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.195→34.232 Å / SU ML: 0.32 / σ(F): 0.04 / Phase error: 21.74 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.006 Å2 / ksol: 0.367 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.195→34.232 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|