+Open data
-Basic information
Entry | Database: PDB / ID: 1h12 | |||||||||
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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 / MOLECULAR REPLACEMENT / Resolution: 1.2 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 | 1h12.cif.gz | 181.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h12.ent.gz | 146.6 KB | Display | PDB format |
PDBx/mmJSON format | 1h12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/1h12 ftp://data.pdbj.org/pub/pdb/validation_reports/h1/1h12 | 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: Sugar | ChemComp-XYP / |
#3: Sugar | ChemComp-XYS / |
#4: 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 WITH 10MG/ML XYLOBIOSE 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: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→20 Å / Num. obs: 141707 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 43.52 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 3.69 / % possible all: 91.9 |
Reflection | *PLUS Highest resolution: 1.2 Å / Lowest resolution: 20 Å / Num. measured all: 1757738 |
Reflection shell | *PLUS Highest resolution: 1.2 Å / % possible obs: 91.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: WILD TYPE WITHOUT LIGAND Resolution: 1.2→65.94 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.752 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / 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: 10.66 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→65.94 Å
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Refine LS restraints |
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