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Yorodumi- PDB-4yz0: C. bescii Family 3 pectate lyase double mutant K108A/E39Q in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yz0 | |||||||||
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Title | C. bescii Family 3 pectate lyase double mutant K108A/E39Q in complex with trigalacturonic acid | |||||||||
Components | Pectate lyase | |||||||||
Keywords | LYASE / PL3 / PARALLEL BETA-HELIX | |||||||||
Function / homology | Function and homology information pectate lyase / pectate lyase activity / pectin catabolic process / hydrolase activity / extracellular region / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Caldicellulosiruptor bescii (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.15 Å | |||||||||
Authors | Alahuhta, P.M. / Lunin, V.V. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: The catalytic mechanism and unique low pH optimum of Caldicellulosiruptor bescii family 3 pectate lyase. Authors: Alahuhta, M. / Taylor, L.E. / Brunecky, R. / Sammond, D.W. / Michener, W. / Adams, M.W. / Himmel, M.E. / Bomble, Y.J. / Lunin, V. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yz0.cif.gz | 217.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yz0.ent.gz | 171 KB | Display | PDB format |
PDBx/mmJSON format | 4yz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/4yz0 ftp://data.pdbj.org/pub/pdb/validation_reports/yz/4yz0 | HTTPS FTP |
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-Related structure data
Related structure data | 4yzaC 4yzqC 4yzxC 4z03C 4z05C 4z06C 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 22104.924 Da / Num. of mol.: 2 / Mutation: K375A, E306Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caldicellulosiruptor bescii (strain ATCC BAA-1888 / DSM 6725 / Z-1320) (bacteria) Strain: ATCC BAA-1888 / DSM 6725 / Z-1320 / Gene: Athe_1854 / Production host: Escherichia coli (E. coli) / References: UniProt: B9MKT4, pectate lyase |
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-Sugars , 4 types, 11 molecules
#2: Polysaccharide | alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-alpha-D-talopyranuronic acid Source method: isolated from a genetically manipulated source | ||
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#3: Polysaccharide | alpha-D-galactopyranuronic acid-(1-4)-alpha-D-galactopyranuronic acid-(1-4)-beta-D-talopyranuronic acid Source method: isolated from a genetically manipulated source | ||
#8: Sugar | #9: Sugar | ChemComp-ADA / |
-Non-polymers , 5 types, 560 molecules
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-IMD / | #6: Chemical | #7: Chemical | ChemComp-MRD / ( #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tris pH 8 and 68% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98397 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98397 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→50.87 Å / Num. obs: 124577 / % possible obs: 95.5 % / Redundancy: 10.3 % / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 1.15→1.17 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 3 / % possible all: 82.9 |
-Processing
Software |
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Refinement | Resolution: 1.15→50 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.329 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 13.123 Å2
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Refinement step | Cycle: 1 / Resolution: 1.15→50 Å
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Refine LS restraints |
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