[English] 日本語
Yorodumi- PDB-3eqz: Crystal structure of a response regulator from Colwellia psychrer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3eqz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a response regulator from Colwellia psychrerythraea | ||||||
Components | Response regulator | ||||||
Keywords | structural genomics / unknown function / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Colwellia psychrerythraea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å | ||||||
Authors | Bonanno, J.B. / Gilmore, M. / Bain, K.T. / Iizuka, M. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a response regulator from Colwellia psychrerythraea Authors: Bonanno, J.B. / Gilmore, M. / Bain, K.T. / Iizuka, M. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3eqz.cif.gz | 61 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3eqz.ent.gz | 45.1 KB | Display | PDB format |
PDBx/mmJSON format | 3eqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/3eqz ftp://data.pdbj.org/pub/pdb/validation_reports/eq/3eqz | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
| ||||||||
Details | possible dimer or tetramer |
-Components
#1: Protein | Mass: 15055.297 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Colwellia psychrerythraea (bacteria) / Strain: 34H / Gene: CPS_1940 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q483U6 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.06 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion / pH: 8 Details: 100mM Hepes pH 8.0, 900mM tri-sodium citrate, Vapor diffusion, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97958 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 11, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97958 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→46.374 Å / Num. all: 17720 / Num. obs: 17720 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.9 % / Biso Wilson estimate: 35.5 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 15.2 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 6.5 / Num. measured all: 38073 / Num. unique all: 2508 / Rsym value: 0.355 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.285 / WRfactor Rwork: 0.24 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.772 / SU B: 5.431 / SU ML: 0.139 / SU R Cruickshank DPI: 0.223 / SU Rfree: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.223 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.16 Å2 / Biso mean: 38.365 Å2 / Biso min: 23.65 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→20 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.15→2.205 Å / Total num. of bins used: 20
|