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Yorodumi- PDB-2jeq: Family 5 xyloglucanase from Paenibacillus pabuli in complex with ... -
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-Basic information
Entry | Database: PDB / ID: 2jeq | |||||||||
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Title | Family 5 xyloglucanase from Paenibacillus pabuli in complex with ligand | |||||||||
Components | XYLOGLUCANASE | |||||||||
Keywords | HYDROLASE / FAMILY 5 / XYLOGLUCANASE / PLANT CELL WALL | |||||||||
Function / homology | Function and homology information xyloglucan-specific endo-beta-1,4-glucanase / cellulase activity / beta-glucosidase activity / cellulose catabolic process / cell surface / extracellular region Similarity search - Function | |||||||||
Biological species | PAENIBACILLUS PABULI (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | |||||||||
Authors | Gloster, T.M. / Ibatullin, F.M. / Macauley, K. / Eklof, J.M. / Roberts, S. / Turkenburg, J.P. / Bjornvad, M.E. / Jorgensen, P.L. / Danielsen, S. / Johansen, K. ...Gloster, T.M. / Ibatullin, F.M. / Macauley, K. / Eklof, J.M. / Roberts, S. / Turkenburg, J.P. / Bjornvad, M.E. / Jorgensen, P.L. / Danielsen, S. / Johansen, K. / Borchert, T.V. / Wilson, K.S. / Brumer, H. / Davies, G.J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Characterization and Three-Dimensional Structures of Two Distinct Bacterial Xyloglucanases from Families Gh5 and Gh12. Authors: Gloster, T.M. / Ibatullin, F.M. / Macauley, K. / Eklof, J.M. / Roberts, S. / Turkenburg, J.P. / Bjornvad, M.E. / Jorgensen, P.L. / Danielsen, S. / Johansen, K. / Borchert, T.V. / Wilson, K.S. ...Authors: Gloster, T.M. / Ibatullin, F.M. / Macauley, K. / Eklof, J.M. / Roberts, S. / Turkenburg, J.P. / Bjornvad, M.E. / Jorgensen, P.L. / Danielsen, S. / Johansen, K. / Borchert, T.V. / Wilson, K.S. / Brumer, H. / Davies, G.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 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 | 2jeq.cif.gz | 94.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jeq.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 2jeq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/2jeq ftp://data.pdbj.org/pub/pdb/validation_reports/je/2jeq | HTTPS FTP |
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-Related structure data
Related structure data | 2jemC 2jenC 2jepSC 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 43969.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PAENIBACILLUS PABULI (bacteria) / Strain: DSM13330 / Production host: BACILLUS SUBTILIS (bacteria) References: UniProt: H9KVH3*PLUS, xyloglucan-specific endo-beta-1,4-glucanase |
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#2: Polysaccharide | beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[beta-D- ...beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
Sequence details | THE FIRST 36 RESIDUES CANNOT BE OBSERVED. THE FIRST 32 OF THESE ARE LIKELY TO BE A SIGNAL PEPTIDE ...THE FIRST 36 RESIDUES CANNOT BE OBSERVED. THE FIRST 32 OF THESE ARE LIKELY TO BE A SIGNAL PEPTIDE CLEAVED DURING EXPRESSION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 32.1 % |
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Crystal grow | pH: 8.5 / Details: 25% PEG 3350, 0.2 M MGCL2, 0.1 M TRIS, PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 4, 2003 / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 22170 / % possible obs: 98.8 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2JEP Resolution: 1.94→61.55 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.9 / SU B: 5.629 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.205 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.94→61.55 Å
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