[English] 日本語
Yorodumi- PDB-1i1w: 0.89A Ultra high resolution structure of a Thermostable Xylanase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i1w | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | 0.89A Ultra high resolution structure of a Thermostable Xylanase from Thermoascus Aurantiacus | |||||||||
Components | ENDO-1,4-BETA-XYLANASEXylanase | |||||||||
Keywords | HYDROLASE / XYLAN DEGRADATION / GLYCOSIDASE / ENZYME / ULTRA HIGH RESOLUTION / CRYO TEMPERATURE / 1 / 4-BETA-XYLAN XYLANOHYDROLASE | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 0.89 Å | |||||||||
Authors | Natesh, R. / Ramakumar, S. / Viswamitra, M.A. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Thermostable xylanase from Thermoascus aurantiacus at ultrahigh resolution (0.89 A) at 100 K and atomic resolution (1.11 A) at 293 K refined anisotropically to small-molecule accuracy. Authors: Natesh, R. / Manikandan, K. / Bhanumoorthy, P. / Viswamitra, M.A. / Ramakumar, S. #1: Journal: J.Mol.Biol. / Year: 1999 Title: Crystal Structure at 1.8 A Resolution and Proposed Amino Acid Sequence of a Thermostable Xylanase from Thermoascus Aurantiascus Authors: Natesh, R. / Bhanumoorthy, P. / Vithayathil, P.J. / Sekar, K. / Ramakumar, S. / Viswamitra, M.A. #2: Journal: J.Mol.Biol. / Year: 1993 Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Crystals of Thermoascus Aurantiacus Xylanase Authors: Viswamitra, M.A. / Bhanumoorthy, P. / Ramakumar, S. / Manjula, M.V. / Vithayathil, P.J. / Murthy, S.K. / Naren, A.P. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1i1w.cif.gz | 193.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1i1w.ent.gz | 153.3 KB | Display | PDB format |
PDBx/mmJSON format | 1i1w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/1i1w ftp://data.pdbj.org/pub/pdb/validation_reports/i1/1i1w | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 32868.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermoascus aurantiacus (fungus) / Strain: STRAIN ISOLATED FROM LOCAL INDIAN SOIL / References: UniProt: P23360, endo-1,4-beta-xylanase |
---|
-Non-polymers , 5 types, 436 molecules
#2: Chemical | ChemComp-UNX / #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-ACN / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.81 % Description: STARTING MODEL WAS LOCALLY AVAILABLE INTERMEDIATE REFINED 1.11 A ROOM TEMPERATURE MODEL. THE STRANGE HETERO MOLECULES SEEN IN 0.89 A HIGH RESOLUTION MAPS, labelled as "UNX 1406 TO UNX ...Description: STARTING MODEL WAS LOCALLY AVAILABLE INTERMEDIATE REFINED 1.11 A ROOM TEMPERATURE MODEL. THE STRANGE HETERO MOLECULES SEEN IN 0.89 A HIGH RESOLUTION MAPS, labelled as "UNX 1406 TO UNX 1410" and "UNX 1411 TO UNX 1418", ARE YET TO BE IDENTIFIED. EOH AND ACN WERE ASSIGNED BASED ON UNRESTRAINED BOND LENGTH AND ANGLES. | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: Ammonium Sulphate, TRIS/HCl, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Viswamitra, M.A., (1993) J.Mol.Biol., 232, 987. | ||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 3, 1999 / Details: MIRROR |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 0.89→35 Å / Num. obs: 177476 / % possible obs: 92 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 32.65 |
Reflection shell | Resolution: 0.89→0.92 Å / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 7.82 / % possible all: 83 |
Reflection | *PLUS Lowest resolution: 35 Å / % possible obs: 92 % / Redundancy: 4.8 % / Num. measured all: 858643 |
Reflection shell | *PLUS % possible obs: 83 % / Rmerge(I) obs: 0.18 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: LOCALLY AVAILABLE INTERMEDIATE REFINED ROOM TEMP. 1.11 A MODEL Resolution: 0.89→10 Å / Num. parameters: 24867 / Num. restraintsaints: 1 / Cross valid method: FREE R / σ(F): 0 StereochEM target val spec case: FINAL 18 CYCLES OF BLOCKED L.S. REFINEMENT (2 CYCLES ON EACH OF 9 BLOCKS) WAS PERFORMED USING SHELXL WITHOUT ANY RESTRAINS. Stereochemistry target values: ENGH AND HUBER Details: AS THE MOLECULE WAS REFINED WITH NO RESTRAINTS THE NON PLANARITY OF THE ARG 124 B CONFORMER AMIDE GROUP MAY NOT BE TAKEN AS TRUE SINCE THE PLANARITY RESTRAINTS WERE NOT IMPOSED TO THIS ...Details: AS THE MOLECULE WAS REFINED WITH NO RESTRAINTS THE NON PLANARITY OF THE ARG 124 B CONFORMER AMIDE GROUP MAY NOT BE TAKEN AS TRUE SINCE THE PLANARITY RESTRAINTS WERE NOT IMPOSED TO THIS SPARCINGLY OCCUPIED DISORDERED ALTERNATE CONFORMER B. CNS 0.4 was also used for refinement.
| |||||||||||||||||||||||||
Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201- | |||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 51 / Occupancy sum hydrogen: 2125 / Occupancy sum non hydrogen: 2765.87 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.89→10 Å
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 0.89→0.92 Å | |||||||||||||||||||||||||
Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Rfactor Rwork: 0.09 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|