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Yorodumi- PDB-1ref: ENDO-1,4-BETA-XYLANASE II COMPLEX WITH 2,3-EPOXYPROPYL-BETA-D-XYLOSIDE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ref | |||||||||
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Title | ENDO-1,4-BETA-XYLANASE II COMPLEX WITH 2,3-EPOXYPROPYL-BETA-D-XYLOSIDE | |||||||||
Components | ENDO-1,4-BETA-XYLANASE IIXylanase | |||||||||
Keywords | HYDROLASE / XYLANASE / XYLAN DEGRADATION | |||||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | Hypocrea jecorina (fungus) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | |||||||||
Authors | Rouvinen, J. / Havukainen, R. / Torronen, A. | |||||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Covalent binding of three epoxyalkyl xylosides to the active site of endo-1,4-xylanase II from Trichoderma reesei. Authors: Havukainen, R. / Torronen, A. / Laitinen, T. / Rouvinen, J. #1: Journal: Embo J. / Year: 1994 Title: Three-Dimensional Structure of Endo-1,4-Beta-Xylanase II from Trichoderma Reesei: Two Conformational States in the Active Site Authors: Torronen, A. / Harkki, A. / Rouvinen, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ref.cif.gz | 85.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ref.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ref.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/1ref ftp://data.pdbj.org/pub/pdb/validation_reports/re/1ref | 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9874, -0.007, 0.158), Vector: |
-Components
#1: Protein | Mass: 20838.436 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hypocrea jecorina (fungus) / Strain: TRICHODERMA REESEI RUT-C30 / References: UniProt: P36217, endo-1,4-beta-xylanase #2: Chemical | ChemComp-BEZ / | #3: Sugar | ChemComp-C3X / ( | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 4.2 / Method: vapor diffusion, hanging drop / Details: Torronen, A., (1993) J. Mol. Biol., 233, 313. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 2, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 30167 / % possible obs: 85.5 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.086 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. measured all: 82450 / Rmerge(I) obs: 0.086 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / % possible obs: 60.3 % |
-Processing
Software |
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Refinement | Resolution: 1.8→8 Å / σ(F): 1
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Displacement parameters | Biso mean: 22.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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