+Open data
-Basic information
Entry | Database: PDB / ID: 2d97 | ||||||
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Title | Structure of VIL-xylanase | ||||||
Components | Endo-1,4-beta-xylanase 2Xylanase | ||||||
Keywords | HYDROLASE / iodo-tyrosine / VAPORIZING IODINE LABELING(VIL) | ||||||
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 / MIRAS / Resolution: 2.01 Å | ||||||
Authors | Miyatake, H. / Hasegawa, T. / Yamano, A. | ||||||
Citation | Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2006 Title: New methods to prepare iodinated derivatives by vaporizing iodine labelling (VIL) and hydrogen peroxide VIL (HYPER-VIL) Authors: Miyatake, H. / Hasegawa, T. / Yamano, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d97.cif.gz | 47.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d97.ent.gz | 36.7 KB | Display | PDB format |
PDBx/mmJSON format | 2d97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/2d97 ftp://data.pdbj.org/pub/pdb/validation_reports/d9/2d97 | 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: 21356.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hypocrea jecorina (fungus) / References: UniProt: P36217, endo-1,4-beta-xylanase |
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#2: 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: 1.95 Å3/Da / Density % sol: 37.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.3 Details: 1.5M ammonium sulfate, 0.1M Na citrate, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 1, 2005 / Details: Osmic Cu CMF |
Radiation | Monochromator: Osmic Cu CMF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→18.98 Å / Num. all: 11332 / Num. obs: 11242 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.5 Å2 |
Reflection shell | Resolution: 2.01→2.13 Å / % possible all: 88.8 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.01→18.98 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 747262.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.5216 Å2 / ksol: 0.424075 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.01→18.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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