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Yorodumi- PDB-1w2p: The 3-dimensional structure of a xylanase (Xyn10A) from Cellvibri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w2p | ||||||
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Title | The 3-dimensional structure of a xylanase (Xyn10A) from Cellvibrio japonicus | ||||||
Components | ENDO-1,4-BETA-XYLANASE A PRECURSOR | ||||||
Keywords | HYDROLASE / XYLANASE / CALCIUM ION / THERMOSTABLE / GLYCOSYLE HYDROLASE / FAMILY 10 / ERROR PRONE PCR | ||||||
Function / homology | Function and homology information cellulose binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | ||||||
Biological species | CELLVIBRIO JAPONICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Taylor, E.J. / Vincent, F. / Gilbert, H.J. / Davies, G.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: The Use of Forced Protein Evolution to Investigate and Improve Stability of Family 10 Xylanases: The Production of Ca2+-Independent Stable Xylanases Authors: Andrews, S. / Taylor, E.J. / Pell, G. / Vincent, F. / Ducros, V. / Davies, G.J. / Lakey, J. / Gilbert, H.J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w2p.cif.gz | 370.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w2p.ent.gz | 309.2 KB | Display | PDB format |
PDBx/mmJSON format | 1w2p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w2p_validation.pdf.gz | 454.9 KB | Display | wwPDB validaton report |
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Full document | 1w2p_full_validation.pdf.gz | 475.2 KB | Display | |
Data in XML | 1w2p_validation.xml.gz | 40.2 KB | Display | |
Data in CIF | 1w2p_validation.cif.gz | 63.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/1w2p ftp://data.pdbj.org/pub/pdb/validation_reports/w2/1w2p | HTTPS FTP |
-Related structure data
Related structure data | 1w2vC 1w32C 1w3hC 1clxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.997, -0.054, 0.048), Vector: |
-Components
#1: Protein | Mass: 38591.676 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 265-611 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) Description: ORGANISM FORMERLY KNOWN AS PSEUDOMONAS FLUORESCENS Plasmid: PET-16B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GM83 DE3 / References: UniProt: P14768, endo-1,4-beta-xylanase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | CATALYTIC ACTIVITY: ENDOHYDROL | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.5 % |
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.933 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→25 Å / Num. obs: 123424 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 3.85 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 8 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 6.76 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CLX Resolution: 1.45→24.62 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.765 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.058 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.54 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→24.62 Å
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Refine LS restraints |
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