[English] 日本語
Yorodumi- PDB-3pz9: Native structure of endo-1,4-beta-D-mannanase from Thermotoga pet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pz9 | ||||||
---|---|---|---|---|---|---|---|
Title | Native structure of endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 | ||||||
Components | Mannan endo-1,4-beta-mannosidase. Glycosyl Hydrolase family 5 | ||||||
Keywords | HYDROLASE / alpha/beta-barrel / manosidase / carbohydrate/sugar binding / secreted | ||||||
Function / homology | Function and homology information mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity Similarity search - Function | ||||||
Biological species | Thermotoga petrophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.42 Å | ||||||
Authors | Santos, C.R. / Meza, A.N. / Paiva, J.H. / Silva, J.C. / Ruller, R. / Prade, R.A. / Squina, F.M. / Murakami, M.T. | ||||||
Citation | Journal: To be Published Title: Structural characterization of a novel hyperthermostable endo-1,4-beta-D-mannanase from Thermotoga petrophila RKU-1 Authors: Santos, C.R. / Meza, A.N. / Paiva, J.H. / Silva, J.C. / Ruller, R. / Prade, R.A. / Squina, F.M. / Murakami, M.T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3pz9.cif.gz | 174.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3pz9.ent.gz | 137.4 KB | Display | PDB format |
PDBx/mmJSON format | 3pz9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3pz9_validation.pdf.gz | 429.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3pz9_full_validation.pdf.gz | 434.5 KB | Display | |
Data in XML | 3pz9_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 3pz9_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/3pz9 ftp://data.pdbj.org/pub/pdb/validation_reports/pz/3pz9 | HTTPS FTP |
-Related structure data
Related structure data | 3pzgC 3pziC 3pzmC 3pznC 3pzoC 3pzqC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 44213.379 Da / Num. of mol.: 1 / Fragment: UNP residues 32-393 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga petrophila (bacteria) / Strain: RKU-1 / Gene: Tpet_1542 / Production host: Escherichia coli (E. coli) References: UniProt: A5IMX7, mannan endo-1,4-beta-mannosidase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.95 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.8 M phosphate, 0.2 M sodium chloride, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 9, 2010 |
Radiation | Monochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.4586 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→40.33 Å / Num. obs: 80074 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 1.42→1.47 Å / % possible all: 86 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIRAS / Resolution: 1.42→40.33 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.786 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 17.845 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→40.33 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.42→1.456 Å / Total num. of bins used: 20
|