+Open data
-Basic information
Entry | Database: PDB / ID: 1dy4 | |||||||||
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Title | CBH1 IN COMPLEX WITH S-PROPRANOLOL | |||||||||
Components | EXOGLUCANASE 1 | |||||||||
Keywords | HYDROLASE / HYDROLASE(O-GLYCOSYL) / CELLULOSE DEAGRADATION / CHIRAL SEPARATION / GLYCOSIDASE / GLYCOPROTEIN | |||||||||
Function / homology | Function and homology information cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / cellulose binding / cellulose catabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | TRICHODERMA REESEI (fungus) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Stahlberg, J. / Henriksson, H. / Divne, C. / Isaksson, R. / Pettersson, G. / Johansson, G. / Jones, T.A. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Structural Basis for Enantiomer Binding and Separation of a Common Beta-Blocker: Crystal Structure of Cellobiohydrolase Cel7A with Bound (S)-Propranolol at 1.9 A Resolution Authors: Stahlberg, J. / Henriksson, H. / Divne, C. / Isaksson, R. / Pettersson, G. / Johansson, G. / Jones, T.A. #1: Journal: J.Mol.Biol. / Year: 1998 Title: High-Resolution Crystal Structures Reveal How a Cellulose Chain is Bound in the 50A Long Tunnel of Cellobiohydrolase I from Trichoderma Reesei Authors: Divne, C. / Stahlberg, J. / Teeri, T.T. / Jones, T.A. #2: Journal: Science / Year: 1994 Title: The Three-Dimensional Crystal Structure of the Catalytic Core of Cellobiohydrolase I from Trichoderma Reesei Authors: Divne, C. / Stahlberg, J. / Reinikainen, T. / Ruohonen, L. / Pettersson, G. / Knowles, J.K. / Teeri, T.T. / Jones, T.A. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: THERE IS A BIFURCATED SHEET IN THIS STRUCTURE. THIS IS REPRESENTED BY ... SHEET DETERMINATION METHOD: THERE IS A BIFURCATED SHEET IN THIS STRUCTURE. THIS IS REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS A AND A1 REPRESENT ONE BIFURCATED SHEET. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dy4.cif.gz | 104.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dy4.ent.gz | 78.4 KB | Display | PDB format |
PDBx/mmJSON format | 1dy4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dy4_validation.pdf.gz | 723.4 KB | Display | wwPDB validaton report |
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Full document | 1dy4_full_validation.pdf.gz | 724.7 KB | Display | |
Data in XML | 1dy4_validation.xml.gz | 20.5 KB | Display | |
Data in CIF | 1dy4_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/1dy4 ftp://data.pdbj.org/pub/pdb/validation_reports/dy/1dy4 | HTTPS FTP |
-Related structure data
Related structure data | 5celS S: Starting model for refinement |
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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: 46010.703 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 18-451 / Source method: isolated from a natural source / Source: (natural) TRICHODERMA REESEI (fungus) / Strain: QM9414 References: UniProt: P62694, cellulose 1,4-beta-cellobiosidase (non-reducing end) | ||||||||
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#2: Sugar | #3: Chemical | ChemComp-SNP / | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | THE I222 CRYSTAL FORM DESCRIBED HERE REPRESENTS THE HIGHER SYMMETRY EQUIVALENT TO THE PSEUDO-I222 ...THE I222 CRYSTAL FORM DESCRIBED HERE REPRESENTS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: HANGING DROPS. EQUAL VOLUMES OF 9 MG/ML PROTEIN/7.5 MM S-PROPRANOLOL AND RESERVOIR SOLUTION CONTAINING 0.1 M MES (PH 7.0), 24% (W/V) MONOMETHYL ETHER PEG 5000, 15% GLYCEROL AND 10 MM COCL2. | ||||||||||||||||||||||||||||||||||||||||||
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: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: R-AXIS IIC / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→33.6 Å / Num. obs: 30518 / % possible obs: 100 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 32.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.095 / Mean I/σ(I) obs: 12.3 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 375375 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5CEL Resolution: 1.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 28512 / Rfactor obs: 0.197 / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.197 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |