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Yorodumi- PDB-2cc0: Family 4 carbohydrate esterase from Streptomyces lividans in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cc0 | ||||||
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Title | Family 4 carbohydrate esterase from Streptomyces lividans in complex with acetate | ||||||
Components | ACETYL-XYLAN ESTERASE | ||||||
Keywords | HYDROLASE / CARBOHYDRATE ESTERASE | ||||||
Function / homology | Function and homology information hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / polysaccharide binding / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | STREPTOMYCES LIVIDANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Taylor, E.J. / Gloster, T.M. / Turkenburg, J.P. / Vincent, F. / Brzozowski, A.M. / Dupont, C. / Shareck, F. / Centeno, M.S.J. / Prates, J.A.M. / Puchart, V. ...Taylor, E.J. / Gloster, T.M. / Turkenburg, J.P. / Vincent, F. / Brzozowski, A.M. / Dupont, C. / Shareck, F. / Centeno, M.S.J. / Prates, J.A.M. / Puchart, V. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Biely, P. / Davies, G.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Structure and Activity of Two Metal-Ion Dependent Acetyl Xylan Esterases Involved in Plant Cell Wall Degradation Reveals a Close Similarity to Peptidoglycan Deacetylases Authors: Taylor, E.J. / Gloster, T.M. / Turkenburg, J.P. / Vincent, F. / Brzozowski, A.M. / Dupont, C. / Shareck, F. / Centeno, M.S.J. / Prates, J.A.M. / Puchart, V. / Ferreira, L.M.A. / Fontes, C.M. ...Authors: Taylor, E.J. / Gloster, T.M. / Turkenburg, J.P. / Vincent, F. / Brzozowski, A.M. / Dupont, C. / Shareck, F. / Centeno, M.S.J. / Prates, J.A.M. / Puchart, V. / Ferreira, L.M.A. / Fontes, C.M.G.A. / Biely, P. / Davies, G.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET 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 | 2cc0.cif.gz | 183.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cc0.ent.gz | 145.2 KB | Display | PDB format |
PDBx/mmJSON format | 2cc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/2cc0 ftp://data.pdbj.org/pub/pdb/validation_reports/cc/2cc0 | HTTPS FTP |
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-Related structure data
Related structure data | 2c71SC 2c79C 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99967, -0.00044, -0.02584), Vector: |
-Components
#1: Protein | Mass: 20614.910 Da / Num. of mol.: 2 / Fragment: RESIDUES 42-236 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES LIVIDANS (bacteria) / Production host: STREPTOMYCES LIVIDANS (bacteria) / References: UniProt: Q54413, acetylxylan esterase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.05 Å3/Da / Density % sol: 39.39 % |
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Crystal grow | pH: 4.5 Details: 7-13% PEG 4K, 0.2 M KBR, 0.1 M NAAC, PH 4.5. PROTEIN 20 MG/ML. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SI (311) MONOCHROMATOR AND SI(111) MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. obs: 51014 / % possible obs: 98 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C71 Resolution: 1.6→65.65 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.893 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.32 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→65.65 Å
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Refine LS restraints |
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