+Open data
-Basic information
Entry | Database: PDB / ID: 1h13 | ||||||
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Title | Structure of a cold-adapted family 8 xylanase | ||||||
Components | ENDO-1,4-BETA-XYLANASEXylanase | ||||||
Keywords | HYDROLASE / XYLAN DEGRADATION / PSYCHROPHILIC / COLD ADAPTATION / TEMPERATURE / GLYCOSYL HYDROLASE / FAMILY 8 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PSEUDOALTEROMONAS HALOPLANKTIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.3 Å | ||||||
Authors | Van Petegem, F. / Collins, T. / Meuwis, M.A. / Feller, G. / Gerday, C. / Van Beeumen, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: The Structure of a Cold-Adapted Family 8 Xylanase at 1.3 A Resolution: Structural Adaptations to Cold and Investigation of the Active Site Authors: Van Petegem, F. / Collins, T. / Meuwis, M.A. / Gerday, C. / Feller, G. / Van Beeumen, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h13.cif.gz | 182 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h13.ent.gz | 151.3 KB | Display | PDB format |
PDBx/mmJSON format | 1h13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/1h13 ftp://data.pdbj.org/pub/pdb/validation_reports/h1/1h13 | 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: 46024.770 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOALTEROMONAS HALOPLANKTIS (bacteria) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q8RJN8, 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: 2.43 Å3/Da / Density % sol: 47.5 % Description: CRYO-ANNEALING LOWERS THE MOSAICITY AND INCREASES THE RESOLUTION LIMIT. | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: TAKE 2 - 10 MG/ML PROTEIN IN 20MM MOPS,50MM NACL, 2% TREHALOSE, PH 7.5, ADD EQUAL VOLUME OF 70% MPD,0.1M PHOSPHATE BUFFER PH 7.0 IN A HANGING DROP EXPERIMENT AT 4 DEGREES CENTIGRADE. | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5 / Method: vapor diffusion, hanging dropDetails: Van Petegem, F., (2002) Acta Crystallogr., D58, 1494. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.8015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8015 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→30 Å / Num. obs: 111031 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 29.63 |
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 3 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 3.56 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.3→65.94 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.296 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.65 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→65.94 Å
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