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Yorodumi- PDB-4z06: C. bescii Family 3 pectate lyase double mutant K108A/R133A in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z06 | ||||||
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Title | C. bescii Family 3 pectate lyase double mutant K108A/R133A in complex with ALPHA-D-GALACTOPYRANURONIC ACID | ||||||
Components | Pectate lyase | ||||||
Keywords | LYASE / PL3 / PARALLEL BETA-HELIX | ||||||
Function / homology | Function and homology information pectate lyase / pectate lyase activity / hydrolase activity / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Caldicellulosiruptor bescii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 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 | 4z06.cif.gz | 111 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z06.ent.gz | 83.5 KB | Display | PDB format |
PDBx/mmJSON format | 4z06.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/4z06 ftp://data.pdbj.org/pub/pdb/validation_reports/z0/4z06 | HTTPS FTP |
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-Related structure data
Related structure data | 4yz0C 4yzaC 4yzqC 4yzxC 4z03C 4z05C 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
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 22019.793 Da / Num. of mol.: 2 / Mutation: K375A, R400A 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 #3: Sugar | |
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-Non-polymers , 4 types, 498 molecules
#2: Chemical | ChemComp-CA / #4: Chemical | ChemComp-MRD / ( | #5: Chemical | ChemComp-MPD / ( #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.1 and 65.9% 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: 1.55→49.8 Å / Num. obs: 49328 / % possible obs: 97.7 % / Redundancy: 13 % / Net I/σ(I): 29.5 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 5.2 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Resolution: 1.55→49.8 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.754 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.088 / 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: 16.884 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→49.8 Å
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Refine LS restraints |
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