+Open data
-Basic information
Entry | Database: PDB / ID: 3uw0 | ||||||
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Title | Pectin methylesterase from Yersinia enterocolitica | ||||||
Components | pectinesterase | ||||||
Keywords | HYDROLASE / right-handed beta-helix / carbohydrate esterase | ||||||
Function / homology | Function and homology information pectinesterase activity / aspartyl esterase activity / cell wall modification Similarity search - Function | ||||||
Biological species | Yersinia enterocolitica subsp. enterocolitica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Abbott, D.W. / Boraston, A.B. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Structure of a pectin methylesterase from Yersinia enterocolitica. Authors: Boraston, A.B. / Abbott, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uw0.cif.gz | 136 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uw0.ent.gz | 105.4 KB | Display | PDB format |
PDBx/mmJSON format | 3uw0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uw/3uw0 ftp://data.pdbj.org/pub/pdb/validation_reports/uw/3uw0 | HTTPS FTP |
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-Related structure data
Related structure data | 1qjvS 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
#1: Protein | Mass: 39784.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia enterocolitica subsp. enterocolitica (bacteria) Strain: 8081 / Gene: YE0549 / Production host: Escherichia coli (E. coli) / References: UniProt: A1JJ76, pectinesterase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.26 Å3/Da / Density % sol: 76.61 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 4.0 M sodium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Aug 14, 2007 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→39.147 Å / Num. obs: 10653 / % possible obs: 99.9 % / Redundancy: 24.7 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 3.5→3.69 Å / Redundancy: 21.1 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 5.9 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QJV Resolution: 3.5→39.147 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.865 / SU B: 38.309 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.949 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→39.147 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.592 Å / Total num. of bins used: 20
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