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Yorodumi- PDB-2wk2: Chitinase A from Serratia marcescens ATCC990 in complex with Chit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wk2 | |||||||||
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Title | Chitinase A from Serratia marcescens ATCC990 in complex with Chitotrio-thiazoline dithioamide. | |||||||||
Components | CHITINASE A | |||||||||
Keywords | HYDROLASE / THIAZOLINES / CHITINASE A / GLYCOSIDASE / CHITIN HYDROLYSIS / CHITIN DEGRADATION / POLYSACCHARIDE DEGRADATION / FAMILY 18 CHITINASES / CARBOHYDRATE METABOLISM | |||||||||
Function / homology | Function and homology information chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | SERRATIA MARCESCENS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||
Authors | Taylor, E.J. / Dennis, R.J. / Macdonald, J.M. / Tarling, C.A. / Knapp, S. / Withers, S.G. / Davies, G.J. | |||||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2010 Title: Chitinase Inhibition by Chitobiose and Chitotriose Thiazolines. Authors: Macdonald, J.M. / Tarling, C.A. / Taylor, E.J. / Dennis, R.J. / Myers, D.S. / Knapp, S. / Davies, G.J. / Withers, S.G. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD" 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. 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 | 2wk2.cif.gz | 133.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wk2.ent.gz | 101.5 KB | Display | PDB format |
PDBx/mmJSON format | 2wk2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/2wk2 ftp://data.pdbj.org/pub/pdb/validation_reports/wk/2wk2 | HTTPS FTP |
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-Related structure data
Related structure data | 2wlyC 2wlzC 2wm0C 1edqS 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
#1: Protein | Mass: 58685.613 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-520 / Source method: isolated from a natural source / Source: (natural) SERRATIA MARCESCENS (bacteria) References: UniProt: A6XFF7, UniProt: P07254*PLUS, chitinase | ||||||||
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#2: Polysaccharide | Type: oligosaccharide / Mass: 456.531 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Chemical | ChemComp-NGT / | #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | THERE ARE KNOWN DISCREPANCIES IN THE SEQUENCE DEPENDING ON WHICH STRAIN OF SERRATIA MARCESCENS THE ...THERE ARE KNOWN DISCREPANC | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.4 Å3/Da / Density % sol: 64 % / Description: NONE |
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Crystal grow | pH: 8 Details: 1.0 M SODIUM CITRATE, 10 MM SODIUM BORATE PH 8.0, DIOXANE 10 % |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.931 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 24, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. obs: 49743 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 5 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.8 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EDQ Resolution: 2.05→109.76 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.469 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 20.822 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→109.76 Å
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