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Yorodumi- PDB-1hjq: Structure of two fungal beta-1,4-galactanases: searching for the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hjq | ||||||
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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 / polysaccharide binding / hydrolase activity, hydrolyzing O-glycosyl compounds / cell wall macromolecule catabolic process Similarity search - Function | ||||||
Biological species | HUMICOLA INSOLENS (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 |
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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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hjq.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hjq.ent.gz | 59.2 KB | Display | PDB format |
PDBx/mmJSON format | 1hjq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/1hjq ftp://data.pdbj.org/pub/pdb/validation_reports/hj/1hjq | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37691.121 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: 2-N-ACETYL-BETA-D-GLUCOSE(A 601) LINKED TO ASN 111 (A 111) Source: (gene. exp.) HUMICOLA INSOLENS (fungus) Description: HUMICOLA INSOLENS IS ALSO KNOWN BY THE NAME MYCELIOPHTHORA THERMOPHILA Production host: ASPERGILLUS ORYZAE (mold) References: UniProt: P83691*PLUS, arabinogalactan endo-beta-1,4-galactanase |
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#2: Sugar | ChemComp-NAG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.88 % |
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Crystal grow | pH: 6.5 Details: 0.1 M SODIUM CACODYLATE PH=6.5 1.4 M SODIUM ACETATE TRIHYDRATE, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.07 |
Detector | Date: Feb 15, 2002 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→20 Å / Num. obs: 13628 / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.14 |
Reflection shell | Resolution: 2.55→2.61 Å / Rmerge(I) obs: 0.44 / % possible all: 90.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MTGAL (TRIS) Resolution: 2.55→19.4 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1245159.86 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 22.2392 Å2 / ksol: 0.392467 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.55→19.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.71 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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