[English] 日本語
Yorodumi- PDB-1goo: Thermostable xylanase I from Thermoascus aurantiacus - Cryocooled... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1goo | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Thermostable xylanase I from Thermoascus aurantiacus - Cryocooled glycerol complex | |||||||||
Components | ENDO-1,4-BETA-XYLANASEXylanase | |||||||||
Keywords | HYDROLASE / FAMILY 10 / PLANT CELL WALL DEGRADATION | |||||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | |||||||||
Biological species | THERMOASCUS AURANTIACUS (fungus) | |||||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.87 Å | |||||||||
Authors | Eckert, K. / Andrei, C. / Larsen, S. / Lo Leggio, L. | |||||||||
Citation | Journal: FEBS Lett. / Year: 2001 Title: Substrate Specificity and Subsite Mobility in T. Aurantiacus Xylanase 10A Authors: Lo Leggio, L. / Kalogiannis, S. / Eckert, K. / Teixeira, S.C.M. / Bhat, M.K. / Andrei, C. / Pickersgill, R.W. / Larsen, S. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Anisotropic Refinement of the Structure of Thermoascus Aurantiacus Xylanase I Authors: Teixeira, S. / Lo Leggio, L. / Pickersgill, R. / Cardin, C. #2: Journal: Proteins / Year: 1999 Title: High Resolution Structure and Sequence of T. Aurantiacus Xylanase I: Implications for the Evolution of Thermostability in Family 10 Xylanases and Enzymes with Beta/Alpha Barrel Architecture Authors: Lo Leggio, L. / Kalogiannis, S. / Bhat, M.K. / Pickersgill, R.W. #3: Journal: Biochem.Soc.Trans. / Year: 1998 Title: Superfamilies: The 4/7 Superfamily of Beta/ Alpha-Barrel Glycosidases and the Right-Handed Parallel Beta-Helix Superfamily Authors: Pickersgill, R. / Harris, G. / Lo Leggio, L. / Mayans, O. / Jenkins, J. #4: Journal: Structural Studies of Xylanases and Endoglucanases / Year: 1997 Title: Structure Solution of Thermoascus Aurantiacus Xylanase. Structural Studies of Xylanases and Endoglucanases Authors: Lo Leggio, L. | |||||||||
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 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1goo.cif.gz | 78.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1goo.ent.gz | 56.3 KB | Display | PDB format |
PDBx/mmJSON format | 1goo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/1goo ftp://data.pdbj.org/pub/pdb/validation_reports/go/1goo | HTTPS FTP |
---|
-Related structure data
Related structure data | 1gokSC 1gomC 1goqC 1gorC 1k6aC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32890.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMOASCUS AURANTIACUS (fungus) / References: UniProt: P23360, endo-1,4-beta-xylanase |
---|---|
#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Sequence details | RESIDUES 1-26 REFER TO THE SIGNAL PEPTIDE IT IS NOT KNOWN IF GLN 303 IS PRESENT IN THE CRYSTAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 32.9 % / Description: THE PH OF CRYSTALLIZATION WAS NOT BUFFERED |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: HANGING DROPS CONTAINING 1:1 RATIO OF 20-30 MG/ML PROTEIN SOLUTION AND RESERVOIR SOLUTION (12 % TO 25 % PEG 6,000). THE CRYSTAL WAS CRYOCOOLED USING GLYCEROL., pH 7.00 |
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→13 Å / Num. obs: 20665 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.064 |
Reflection shell | Resolution: 1.87→1.9 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.315 / % possible all: 96.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1GOK Resolution: 1.87→12.93 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 624834.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.2229 Å2 / ksol: 0.417659 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→12.93 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.87→1.99 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|