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Yorodumi- PDB-2wlz: Chitinase A from Serratia marcescens ATCC990 in complex with Chit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wlz | ||||||
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Title | Chitinase A from Serratia marcescens ATCC990 in complex with Chitobio- thiazoline. | ||||||
Components | CHITINASE A | ||||||
Keywords | HYDROLASE / HYDROLASE A / 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: 1.82 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 | 2wlz.cif.gz | 131.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wlz.ent.gz | 99.5 KB | Display | PDB format |
PDBx/mmJSON format | 2wlz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wlz_validation.pdf.gz | 312.5 KB | Display | wwPDB validaton report |
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Full document | 2wlz_full_validation.pdf.gz | 312.8 KB | Display | |
Data in XML | 2wlz_validation.xml.gz | 1.8 KB | Display | |
Data in CIF | 2wlz_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/2wlz ftp://data.pdbj.org/pub/pdb/validation_reports/wl/2wlz | HTTPS FTP |
-Related structure data
Related structure data | 2wk2C 2wlyC 2wm0C 1edqS C: citing same article (ref.) 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 59756.781 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-520 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Plasmid: PET22B (NOVAGEN) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A6XFF7, UniProt: P07254*PLUS, chitinase |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 451 molecules
#2: Chemical | ChemComp-DIO / #3: Chemical | #4: Chemical | ChemComp-NGT / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THERE ARE KNOWN DISCREPANCIES IN THE SEQUENCE DEPENDING ON WHICH STRAIN OF SERRATIA MARCESCENS THE ...THERE ARE KNOWN DISCREPANC |
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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: 3.36 Å3/Da / Density % sol: 63.45 % / Description: NONE |
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Crystal grow | pH: 8 Details: 1.0M SODIUM CITRATE 10MM SODIUM BORATE PH8 DIOXANE 20%, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 15, 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: 1.81→43.9 Å / Num. obs: 69869 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.81→1.91 Å / Redundancy: 2.6 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 0.8 / % possible all: 81.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EDQ Resolution: 1.82→109.76 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.914 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.109 / 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: 19.643 Å2
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Refinement step | Cycle: LAST / Resolution: 1.82→109.76 Å
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Refine LS restraints |
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