+Open data
-Basic information
Entry | Database: PDB / ID: 2ewh | ||||||
---|---|---|---|---|---|---|---|
Title | Carboxysome protein CsoS1A from Halothiobacillus neapolitanus | ||||||
Components | Major carboxysome shell protein 1A | ||||||
Keywords | CARBOXYSOME / bacterial microcompartment domain | ||||||
Function / homology | Function and homology information structural constituent of carboxysome shell / carboxysome / carbon fixation Similarity search - Function | ||||||
Biological species | Halothiobacillus neapolitanus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Tsai, Y. / Sawaya, M.R. / Kerfeld, C.A. / Yeates, T.O. | ||||||
Citation | Journal: Plos Biol. / Year: 2007 Title: Structural Analysis of CsoS1A and the Protein Shell of the Halothiobacillus neapolitanus Carboxysome. Authors: Tsai, Y. / Sawaya, M.R. / Cannon, G.C. / Cai, F. / Williams, E.B. / Heinhorst, S. / Kerfeld, C.A. / Yeates, T.O. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ewh.cif.gz | 31.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ewh.ent.gz | 20.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ewh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ewh_validation.pdf.gz | 445.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2ewh_full_validation.pdf.gz | 445.9 KB | Display | |
Data in XML | 2ewh_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | 2ewh_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/2ewh ftp://data.pdbj.org/pub/pdb/validation_reports/ew/2ewh | HTTPS FTP |
-Related structure data
Related structure data | 2g13C 2a10S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| x 6|||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
| |||||||||
Details | The biological assembly is a hexamer generated from the monomer in the asymmetric unit by the operations: -Y,X-Y,Z; Y-X,-X,Z; -X,-Y,Z; Y,Y-X,Z; X-Y,X,Z. |
-Components
#1: Protein | Mass: 9973.478 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Halothiobacillus neapolitanus (bacteria) Gene: csoS1A / Plasmid: pProEx-Htb / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P45689 |
---|---|
#2: Chemical | ChemComp-TRS / |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.5 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 Details: 30% PEG 400, 0.1M 2(cyclohexylamino)ethanosulfonic acid, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2005 |
Radiation | Monochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→90 Å / Num. all: 13685 / Num. obs: 13685 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.072 / Χ2: 1.12 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.395 / Num. unique all: 1025 / Χ2: 1.067 / % possible all: 71.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2A10 Resolution: 1.4→57.54 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.542 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.091 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.4 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→57.54 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.402→1.439 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 19.4548 Å / Origin y: 8.7313 Å / Origin z: -12.7841 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection: ALL |