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Yorodumi- PDB-1w3l: ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN COMPLEX WITH C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w3l | |||||||||
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Title | ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN COMPLEX WITH CELLOTRI DERIVED-TETRAHYDROOXAZINE | |||||||||
Components | ENDOGLUCANASE 5A | |||||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE / CELLULOSE DEGRADATION / ENDOGLUCANASE / FAMILY 5 / TETRAHYDROOXAZINE | |||||||||
Function / homology | Function and homology information cellulase / cellulase activity / cellulose catabolic process / carbohydrate binding / extracellular region Similarity search - Function | |||||||||
Biological species | BACILLUS AGARADHAERENS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å | |||||||||
Authors | Gloster, T.M. / Macdonald, J.M. / Tarling, C.A. / Stick, R.V. / Withers, S.W. / Davies, G.J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structural, Thermodynamic, and Kinetic Analyses of Tetrahydrooxazine-Derived Inhibitors Bound to {Beta}-Glucosidases Authors: Gloster, T.M. / Macdonald, J.M. / Tarling, C.A. / Stick, R.V. / Withers, S.W. / Davies, G.J. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-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 | 1w3l.cif.gz | 169.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w3l.ent.gz | 134.7 KB | Display | PDB format |
PDBx/mmJSON format | 1w3l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w3l_validation.pdf.gz | 806.1 KB | Display | wwPDB validaton report |
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Full document | 1w3l_full_validation.pdf.gz | 812.3 KB | Display | |
Data in XML | 1w3l_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 1w3l_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/1w3l ftp://data.pdbj.org/pub/pdb/validation_reports/w3/1w3l | HTTPS FTP |
-Related structure data
Related structure data | 1w3jC 1w3kC 1ocqS 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 33998.023 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE, RESIDUES 27-329 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS AGARADHAERENS (bacteria) / Plasmid: THERMAMYL-AMYLASE PROMOT / Production host: BACILLUS SUBTILIS (bacteria) / Strain (production host): PL2306 / References: UniProt: O85465, cellulase |
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#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellobiose |
-Non-polymers , 4 types, 610 molecules
#3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-OXZ / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE FIRST 26 RESIDUES IN THE DATABASE CORRESPOND TO THE PROSEQUENCE. OUR NUMBERING BEGINS AT THE ...THE FIRST 26 RESIDUES IN THE DATABASE CORRESPOND |
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-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: 42 % / Description: STRUCTURE ISOMORPHOUS WITH STARTING MODEL |
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Crystal grow | pH: 5 Details: PROTEIN CONCENTRATION 20MG/ML, 1.3 M AMMONIUM SULPHATE PH 5.0, 25% GLYCEROL AS CRYOPROTECTANT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 15, 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: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→40 Å / Num. obs: 132684 / % possible obs: 98.9 % / Redundancy: 8 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 29.5 |
Reflection shell | Resolution: 1.04→1.06 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 3.1 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OCQ Resolution: 1.04→51.5 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.479 / SU ML: 0.011 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.02 / 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: 8.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.04→51.5 Å
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Refine LS restraints |
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