[English] 日本語
Yorodumi- PDB-2e6c: Crystal structure of the stationary phase survival protein SurE f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e6c | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the stationary phase survival protein SurE from Thermus thermophilus HB8 cocrystallized with manganese and AMP | ||||||
Components | 5'-nucleotidase surE | ||||||
Keywords | HYDROLASE / SurE protein / cocrystal structure with manganese ion and AMP | ||||||
Function / homology | Function and homology information 3'-nucleotidase activity / exopolyphosphatase activity / XMP 5'-nucleosidase activity / 5'-nucleotidase / nucleotide binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Iwasaki, W. / Miki, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Crystal Structure of the Stationary Phase Survival Protein SurE with Metal Ion and AMP Authors: Iwasaki, W. / Miki, K. | ||||||
History |
| ||||||
Remark 300 | BIOMOLECULE 1 This entry contains the crystallographic asymmetric unit which consists of 4 chain(s) ...BIOMOLECULE 1 This entry contains the crystallographic asymmetric unit which consists of 4 chain(s) forming a tetramer. This protein is in a dimer-tetramer equilibrium in solution. It is unknown whether this protein is functional as a dimer or a tetramer. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2e6c.cif.gz | 200.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2e6c.ent.gz | 159.7 KB | Display | PDB format |
PDBx/mmJSON format | 2e6c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2e6c_validation.pdf.gz | 473.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2e6c_full_validation.pdf.gz | 491.7 KB | Display | |
Data in XML | 2e6c_validation.xml.gz | 38.6 KB | Display | |
Data in CIF | 2e6c_validation.cif.gz | 53.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/2e6c ftp://data.pdbj.org/pub/pdb/validation_reports/e6/2e6c | HTTPS FTP |
-Related structure data
Related structure data | 2e69SC 2e6bC 2e6eC 2e6gC 2e6hC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | probably tetramer |
-Components
#1: Protein | Mass: 26625.287 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53W92, 5'-nucleotidase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.5 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 Details: 0.1M Tris-HCl pH8.5, 0.75M ammonium sulfate, 10% glycerol, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 26, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 83555 / % possible obs: 100 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.05→2.12 Å / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 7.5 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2E69 Resolution: 2.05→46.56 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3382480.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.5791 Å2 / ksol: 0.374002 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.3 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→46.56 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|