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Yorodumi- PDB-4yzx: C. bescii Family 3 pectate lyase double mutant K108A/D107N in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yzx | |||||||||
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Title | C. bescii Family 3 pectate lyase double mutant K108A/D107N 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: 1.25 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 | 4yzx.cif.gz | 207.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yzx.ent.gz | 165.6 KB | Display | PDB format |
PDBx/mmJSON format | 4yzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/4yzx ftp://data.pdbj.org/pub/pdb/validation_reports/yz/4yzx | HTTPS FTP |
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-Related structure data
Related structure data | 4yz0C 4yzaC 4yzqC 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, D374N 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 , 3 types, 5 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Sugar | ChemComp-GTR / | #9: Sugar | |
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-Non-polymers , 6 types, 596 molecules
#3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | ChemComp-MPD / ( #6: Chemical | #7: Chemical | #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: 2.09 Å3/Da / Density % sol: 41.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris pH 8 and 61% 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: 1.25→34.58 Å / Num. obs: 91778 / % possible obs: 95.1 % / Redundancy: 6.8 % / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.25→1.27 Å / Mean I/σ(I) obs: 1.9 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Resolution: 1.25→34.58 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.675 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.043 / 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: 17.05 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→34.58 Å
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Refine LS restraints |
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