+Open data
-Basic information
Entry | Database: PDB / ID: 6ojl | |||||||||
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Title | Structure of YePL2A R194K in Complex with Pentagalacturonic Acid | |||||||||
Components | Periplasmic pectate lyase | |||||||||
Keywords | LYASE / pectin / (alpha/alpha)8 | |||||||||
Function / homology | Function and homology information carbon-oxygen lyase activity, acting on polysaccharides / pectin catabolic process / periplasmic space Similarity search - Function | |||||||||
Biological species | Yersinia enterocolitica (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Jones, D.R. / Abbott, D.W. | |||||||||
Citation | Journal: J.Struct.Biol. / Year: 2019 Title: A surrogate structural platform informed by ancestral reconstruction and resurrection of a putative carbohydrate binding module hybrid illuminates the neofunctionalization of a pectate lyase. Authors: Jones, D.R. / McLean, R. / Hobbs, J.K. / 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 | 6ojl.cif.gz | 137.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ojl.ent.gz | 103.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ojl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/6ojl ftp://data.pdbj.org/pub/pdb/validation_reports/oj/6ojl | HTTPS FTP |
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-Related structure data
Related structure data | 6ojkC 2v8kS 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: 64313.789 Da / Num. of mol.: 1 / Mutation: R194K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Gene: pelY, ERS137951_00187 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A0T9S209 | ||
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#2: Polysaccharide | alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D- ...alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-beta-D-galactopyranuronic acid Source method: isolated from a genetically manipulated source | ||
#3: Chemical | #4: 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: 2.78 Å3/Da / Density % sol: 55.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 1500, Sodium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Oct 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→46.53 Å / Num. obs: 114656 / % possible obs: 99.56 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.04494 / Net I/σ(I): 17.82 |
Reflection shell | Resolution: 1.5→1.5171 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.6217 / Mean I/σ(I) obs: 2.63 / Num. unique obs: 3554 / % possible all: 99.87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2v8k Resolution: 1.5→46.507 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / Phase error: 17.59
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→46.507 Å
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Refine LS restraints |
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LS refinement shell |
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