+Open data
-Basic information
Entry | Database: PDB / ID: 3wt3 | ||||||
---|---|---|---|---|---|---|---|
Title | New crystal form of a hyperthermophilic endocellulase | ||||||
Components | Endoglucanase A | ||||||
Keywords | HYDROLASE / Beta-jelly roll / Glycoside hydrolase | ||||||
Function / homology | Function and homology information cellulase activity / polysaccharide catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.68 Å | ||||||
Authors | Kataoka, M. / Ishikawa, K. | ||||||
Citation | Journal: To be Published Title: A new crystal form of a hyperthermophilic endocellulase Authors: Kataoka, M. / Ishikawa, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3wt3.cif.gz | 138.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3wt3.ent.gz | 106.3 KB | Display | PDB format |
PDBx/mmJSON format | 3wt3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wt3_validation.pdf.gz | 459.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3wt3_full_validation.pdf.gz | 475.5 KB | Display | |
Data in XML | 3wt3_validation.xml.gz | 30.1 KB | Display | |
Data in CIF | 3wt3_validation.cif.gz | 43.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/3wt3 ftp://data.pdbj.org/pub/pdb/validation_reports/wt/3wt3 | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 50 - 319 / Label seq-ID: 50 - 319
|
-Components
#1: Protein | Mass: 36015.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: eglA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9V2T0, cellulase #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.08 % / Mosaicity: 0.284 ° / Mosaicity esd: 0.002 ° |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M CHC buffer, 0.2M lithium sulfate, 5%(v/v) ethanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Nov 21, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.68→50 Å / Num. obs: 81623 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.068 / Χ2: 1.03 / Net I/σ(I): 14.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→43.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.2478 / WRfactor Rwork: 0.2044 / FOM work R set: 0.8563 / SU B: 1.838 / SU ML: 0.062 / SU R Cruickshank DPI: 0.0912 / SU Rfree: 0.0949 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES
| |||||||||||||||||||||||||||||||||||||||||||||
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 max: 89.9 Å2 / Biso mean: 27.321 Å2 / Biso min: 7.94 Å2
| |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.68→43.01 Å
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Ens-ID: 1 / Number: 346 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.19 Å / Weight position: 0.05
| |||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.679→1.723 Å / Total num. of bins used: 20
|