[English] 日本語
Yorodumi- PDB-2jic: High resolution structure of xylanase-II from one micron beam exp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jic | ||||||
---|---|---|---|---|---|---|---|
Title | High resolution structure of xylanase-II from one micron beam experiment | ||||||
Components | XYLANASE-II | ||||||
Keywords | HYDROLASE / ENDONUCLEASE / XYLAN DEGRADATION / FUNGI / XYLAN / MICROBEAM / GLYCOSIDASE | ||||||
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 | TRICHODERMA LONGIBRACHIATUM (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Moukhametzianov, R. / Burghammer, M. / Edwards, P.C. / Petitdemange, S. / Popov, D. / Fransen, M. / Schertler, G.F. / Riekel, C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Protein Crystallography with a Micrometre-Sized Synchrotron-Radiation Beam. Authors: Moukhametzianov, R. / Burghammer, M. / Edwards, P.C. / Petitdemange, S. / Popov, D. / Fransen, M. / Mcmullan, G. / Schertler, G.F. / Riekel, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2jic.cif.gz | 53.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2jic.ent.gz | 38.1 KB | Display | PDB format |
PDBx/mmJSON format | 2jic.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/2jic ftp://data.pdbj.org/pub/pdb/validation_reports/ji/2jic | HTTPS FTP |
---|
-Related structure data
Related structure data | 2d97S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20858.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TRICHODERMA LONGIBRACHIATUM (fungus) / References: UniProt: F8W669*PLUS, endo-1,4-beta-xylanase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 38.4 % / Description: NONE |
---|---|
Crystal grow | pH: 5.5 Details: 2M AMMONIUM SULPHATE, 100 MM MES PH 5.5 AND 0.5 M MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9763 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 7, 2006 / Details: KB MIRROR |
Radiation | Monochromator: SI-111 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→100 Å / Num. obs: 26872 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 13.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 7.1 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2D97 Resolution: 1.5→11.05 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1105231.34 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: XYLANASE-II WAS USED AS A TEST CRYSTAL FOR THE ONE MICRON SIZE BEAM CRYSTALLOGRAPHY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.4816 Å2 / ksol: 0.484548 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.2 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→11.05 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|