+Open data
-Basic information
Entry | Database: PDB / ID: 1gny | |||||||||
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Title | xylan-binding module CBM15 | |||||||||
Components | XYLANASE 10C | |||||||||
Keywords | CARBOHYDRATE-BINDING MODULE / XYLAN / XYLOOLIGOSACCHARIDE / XYLANASE / CATALYSIS | |||||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / cell outer membrane Similarity search - Function | |||||||||
Biological species | PSEUDOMONAS CELLULOSA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | |||||||||
Authors | Szabo, S. / Jamal, S. / Xie, H. / Charnock, S.J. / Bolam, D.N. / Gilbert, H.J. / Davies, G.J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Structure of a Family 15 Carbohydrate-Binding Module in Complex with Xylopentaose: Evidence that Xylan Binds in an Approximate Three-Fold Helical Conformation Authors: Szabo, L. / Jamal, S. / Xie, H. / Charnock, S.J. / Bolam, D.N. / Gilbert, H.J. / Davies, G.J. | |||||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gny.cif.gz | 49.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gny.ent.gz | 33.7 KB | Display | PDB format |
PDBx/mmJSON format | 1gny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gny_validation.pdf.gz | 634 KB | Display | wwPDB validaton report |
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Full document | 1gny_full_validation.pdf.gz | 634.1 KB | Display | |
Data in XML | 1gny_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 1gny_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/1gny ftp://data.pdbj.org/pub/pdb/validation_reports/gn/1gny | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15984.539 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE BINDING MODULE 15, RESIDUES (91-244) Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS CELLULOSA (bacteria) / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): DE3-PLYSS / References: UniProt: Q59675, endo-1,4-beta-xylanase |
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#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose- ...beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Sequence details | CBM15 IS A SMALL PORTION OF THIS ORF CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.03 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 Details: 0.2M NH4OAC,0.1M NA CITRATE PH 5.6, 30% POLYETHYLENE GLYCOL 4000 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
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: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Detector: CCD / Date: Mar 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→50 Å / Num. obs: 21535 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.63→1.69 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3 / % possible all: 80 |
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 98 % |
Reflection shell | *PLUS % possible obs: 80 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PARTIAL MODEL (UNPUBLISHED) Resolution: 1.63→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.535 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.077 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→50 Å
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Refine LS restraints |
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