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Yorodumi- PDB-1gor: THERMOSTABLE XYLANASE I FROM THERMOASCUS AURANTIACUS - XYLOBIOSE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gor | ||||||||||||
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Title | THERMOSTABLE XYLANASE I FROM THERMOASCUS AURANTIACUS - XYLOBIOSE COMPLEX AT 100 K | ||||||||||||
Components | ENDO-1,4-BETA-XYLANASEXylanase | ||||||||||||
Keywords | HYDROLASE / XYLANASE / FAMILY 10 / PLANT CELL WALL DEGRADATION / THERMOSTABLE | ||||||||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å | ||||||||||||
Authors | Lo Leggio, L. / Larsen, S. | ||||||||||||
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. | ||||||||||||
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 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 |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gor.cif.gz | 78.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gor.ent.gz | 55.4 KB | Display | PDB format |
PDBx/mmJSON format | 1gor.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/1gor ftp://data.pdbj.org/pub/pdb/validation_reports/go/1gor | HTTPS FTP |
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-Related structure data
Related structure data | 1gokSC 1gomC 1gooC 1goqC 1k6aC C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 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 |
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#2: Polysaccharide | beta-D-xylopyranose-(1-4)-alpha-D-xylopyranose Source method: isolated from a genetically manipulated source |
#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 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 32.9 % / Description: THE PH OF CRYSTALLIZATION WAS NOT BUFFERED |
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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 WITH GLYCEROL AND 0.5 M XYLOBIOSE, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→16 Å / Num. obs: 26202 / % possible obs: 95 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.063 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2 % / Rmerge(I) obs: 0.343 / % possible all: 75.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1GOK Resolution: 1.7→16 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 66.6 Å2 / ksol: 0.436 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→16 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP |