[English] 日本語
Yorodumi- PDB-4evu: Crystal structure of C-terminal domain of putative periplasmic pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4evu | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of C-terminal domain of putative periplasmic protein ydgH from S. enterica | ||||||
Components | Putative periplasmic protein ydgH | ||||||
Keywords | Structural Genomics / Unknown Function / PSI-Biology / Program for the Characterization of Secreted Effector Proteins / PCSEP / Midwest Center for Structural Genomics / MCSG / secreted effector | ||||||
Function / homology | Function and homology information YdgH protein / YdgH/BhsA/McbA-like domain / YdgH-like superfamily / YdgH/BhsA/McbA-like domain / Flavin-binding protein dodecin / Dodecin-like / Dodecin subunit-like / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å | ||||||
Authors | Michalska, K. / Cui, H. / Xu, X. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Savchenko, A. / Adkins, J.N. / Joachimiak, A. ...Michalska, K. / Cui, H. / Xu, X. / Brown, R.N. / Cort, J.R. / Heffron, F. / Nakayasu, E.S. / Savchenko, A. / Adkins, J.N. / Joachimiak, A. / Program for the Characterization of Secreted Effector Proteins (PCSEP) / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Plos One / Year: 2014 Title: Structural and Functional Characterization of DUF1471 Domains of Salmonella Proteins SrfN, YdgH/SssB, and YahO. Authors: Eletsky, A. / Michalska, K. / Houliston, S. / Zhang, Q. / Daily, M.D. / Xu, X. / Cui, H. / Yee, A. / Lemak, A. / Wu, B. / Garcia, M. / Burnet, M.C. / Meyer, K.M. / Aryal, U.K. / Sanchez, O. ...Authors: Eletsky, A. / Michalska, K. / Houliston, S. / Zhang, Q. / Daily, M.D. / Xu, X. / Cui, H. / Yee, A. / Lemak, A. / Wu, B. / Garcia, M. / Burnet, M.C. / Meyer, K.M. / Aryal, U.K. / Sanchez, O. / Ansong, C. / Xiao, R. / Acton, T.B. / Adkins, J.N. / Montelione, G.T. / Joachimiak, A. / Arrowsmith, C.H. / Savchenko, A. / Szyperski, T. / Cort, J.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4evu.cif.gz | 71.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4evu.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 4evu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/4evu ftp://data.pdbj.org/pub/pdb/validation_reports/ev/4evu | HTTPS FTP |
---|
-Related structure data
Related structure data | 2m2jC 2ma4C 2ma8C C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 8259.871 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Strain: LT2 / Gene: STM1478, ydgH / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q8ZPL1 #2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.37 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M Na Citrate , 0.2 M K/Na tartrate, 1.9 M (NH4)2SO4, 5% Glycerol, 1/210 trypsin, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2011 / Details: mirrors | |||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
| |||||||||||||||
Reflection | Resolution: 1.45→50 Å / Num. all: 26432 / Num. obs: 26374 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 25.2 | |||||||||||||||
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1279 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.45→36.92 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.021 / SU ML: 0.033 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.013 / ESU R Free: 0.012 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGEN ATOMS HAVE BEEN ADDED AT THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.404 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→36.92 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.45→1.514 Å / Total num. of bins used: 12
|