[English] 日本語
Yorodumi- PDB-1hjs: Structure of two fungal beta-1,4-galactanases: searching for the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hjs | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of two fungal beta-1,4-galactanases: searching for the basis for temperature and pH optimum. | ||||||
Components | BETA-1,4-GALACTANASE | ||||||
Keywords | HYDROLASE / BETA-1 / 4-GALACTANASES / FAMILY 53 GLYCOSIDE HYDROLASE / THERMOSTABILITY / PH OPTIMUM / CLAN GH-A / THERMOPHILE / ALKALOPHILE | ||||||
Function / homology | Function and homology information arabinogalactan endo-beta-1,4-galactanase / arabinogalactan endo-1,4-beta-galactosidase activity / glucosidase activity / pectin catabolic process / polysaccharide binding / hydrolase activity, hydrolyzing O-glycosyl compounds / cell wall macromolecule catabolic process Similarity search - Function | ||||||
Biological species | THIELAVIA HETEROTHALLICA (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.87 Å | ||||||
Authors | Le Nours, J. / Ryttersgaard, C. / Lo Leggio, L. / Ostergaard, P.R. / Borchert, T.V. / Christensen, L.L.H. / Larsen, S. | ||||||
Citation | Journal: Protein Sci. / Year: 2003 Title: Structure of Two Fungal Beta-1,4-Galactanases: Searching for the Basis for Temperature and Ph Optimum Authors: Le Nours, J. / Ryttersgaard, C. / Lo Leggio, L. / Ostergaard, P.R. / Borchert, T.V. / Christensen, L.L.H. / Larsen, S. | ||||||
History |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1hjs.cif.gz | 272 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1hjs.ent.gz | 225.6 KB | Display | PDB format |
PDBx/mmJSON format | 1hjs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hjs_validation.pdf.gz | 514.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1hjs_full_validation.pdf.gz | 534.3 KB | Display | |
Data in XML | 1hjs_validation.xml.gz | 54.5 KB | Display | |
Data in CIF | 1hjs_validation.cif.gz | 76.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/1hjs ftp://data.pdbj.org/pub/pdb/validation_reports/hj/1hjs | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
-Protein / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 36841.055 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: 2-N-ACETYL-BETA-D-GLUCOSE(RESIDUE 601) LINKED TO ASN 111 IN THE FOUR MOLECULES Source: (gene. exp.) THIELAVIA HETEROTHALLICA (fungus) Description: MYCELIOPHTHORA THERMOPHILA IS THE ANAMORPH NAME WHILST THIELAVIA HETEROTHALLIC IS THE TELEOMORPH NAME Production host: ASPERGILLUS ORYZAE (mold) References: UniProt: P83692*PLUS, arabinogalactan endo-beta-1,4-galactanase #2: Sugar | ChemComp-NAG / |
---|
-Non-polymers , 4 types, 668 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-EPE / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.38 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 Details: 30% PEG4000, 0.2 M AMMONIUM SULPHATE, 0.1M HEPES PH=7.5, pH 7.50 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.07 |
Detector | Date: Nov 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→20 Å / Num. obs: 114360 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.076 |
Reflection shell | Resolution: 1.88→1.95 Å / Rmerge(I) obs: 0.417 / % possible all: 89 |
Reflection | *PLUS Highest resolution: 1.88 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 89 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 61.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: OTHER / Resolution: 1.87→19.84 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 381740.82 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 40.4333 Å2 / ksol: 0.393179 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.9 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→19.84 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.87→1.99 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.88 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.194 / Rfactor Rfree: 0.208 / Rfactor Rwork: 0.194 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.257 / Rfactor Rwork: 0.243 |