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Yorodumi- PDB-1xyz: A COMMON PROTEIN FOLD AND SIMILAR ACTIVE SITE IN TWO DISTINCT FAM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xyz | ||||||
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Title | A COMMON PROTEIN FOLD AND SIMILAR ACTIVE SITE IN TWO DISTINCT FAMILIES OF BETA-GLYCANASES | ||||||
Components | 1,4-BETA-D-XYLAN-XYLANOHYDROLASE | ||||||
Keywords | GLYCOSYLTRANSFERASE / GLYCOSYL HYDROLASE / XYLANASE / FAMILY F/10 OF GLYCOSYL HYDROLASES / CLOSTRIDIUM THERMOCELLUM | ||||||
Function / homology | Function and homology information xylan endo-1,3-beta-xylosidase activity / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding Similarity search - Function | ||||||
Biological species | Clostridium thermocellum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å | ||||||
Authors | Alzari, P.M. / Spinelli, S. / Dominguez, R. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1995 Title: A common protein fold and similar active site in two distinct families of beta-glycanases. Authors: Dominguez, R. / Souchon, H. / Spinelli, S. / Dauter, Z. / Wilson, K.S. / Chauvaux, S. / Beguin, P. / Alzari, P.M. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallization and Preliminary Diffraction Analysis of the Catalytic Domain of Xylanase Z from Clostridium Thermocellum Authors: Souchon, H. / Spinelli, S. / Beguin, P. / Alzari, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xyz.cif.gz | 146.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xyz.ent.gz | 114.8 KB | Display | PDB format |
PDBx/mmJSON format | 1xyz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/1xyz ftp://data.pdbj.org/pub/pdb/validation_reports/xy/1xyz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Atom site foot note | 1: HIS A 596 - THR A 597 OMEGA = 0.11 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: HIS B 596 - THR B 597 OMEGA = 0.29 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99997, 0.00357, 0.00622), Vector: Details | MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 516 .. A 835 B 516 .. B 835 0.287 | |
-Components
#1: Protein | Mass: 39434.227 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: NCIB 10682 / Plasmid: PCT1214 (PUC8) / Production host: Escherichia coli (E. coli) / References: UniProt: P10478, endo-1,4-beta-xylanase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.63 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 24 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.92 Å |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Num. obs: 11704 / % possible obs: 96.4 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.083 |
Reflection | *PLUS Highest resolution: 1.4 Å / Lowest resolution: 10 Å / Num. obs: 117046 / Num. measured all: 343930 / Rmerge(I) obs: 0.083 |
-Processing
Software |
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Refinement | Resolution: 1.4→10 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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