+Open data
-Basic information
Entry | Database: PDB / ID: 4z05 | ||||||
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Title | C. bescii Family 3 pectate lyase mutant E84A | ||||||
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 / Resolution: 1.5 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 | 4z05.cif.gz | 107 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z05.ent.gz | 86.3 KB | Display | PDB format |
PDBx/mmJSON format | 4z05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/4z05 ftp://data.pdbj.org/pub/pdb/validation_reports/z0/4z05 | HTTPS FTP |
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-Related structure data
Related structure data | 4yz0C 4yzaC 4yzqC 4yzxC 4z03C 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: 22105.975 Da / Num. of mol.: 2 / Mutation: E351A 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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-Non-polymers , 5 types, 505 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-MPD / ( #5: Chemical | #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: 2.32 Å3/Da / Density % sol: 47.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.4 and 66.8% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Sep 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 66566 / % possible obs: 99.7 % / Redundancy: 6.42 % / Net I/σ(I): 17.29 |
Reflection shell | Resolution: 1.5→1.6 Å / Redundancy: 3.22 % / Mean I/σ(I) obs: 2.71 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.371 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.07 / 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: 15.956 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→50 Å
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Refine LS restraints |
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