+Open data
-Basic information
Entry | Database: PDB / ID: 6ha5 | ||||||
---|---|---|---|---|---|---|---|
Title | AFGH61B L90V/D131S/M134L/A141W VARIANT | ||||||
Components | Endoglucanase, putative | ||||||
Keywords | OXIDOREDUCTASE / lytic polysaccharide monooxygenase | ||||||
Function / homology | Function and homology information cellulose binding / cellulase / cellulase activity / cellulose catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Neosartorya fumigata (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Lo Leggio, L. / Poulsen, J.C.N. | ||||||
Citation | Journal: Carbohydr. Res. / Year: 2018 Title: Structure of a lytic polysaccharide monooxygenase from Aspergillus fumigatus and an engineered thermostable variant. Authors: Lo Leggio, L. / Weihe, C.D. / Poulsen, J.N. / Sweeney, M. / Rasmussen, F. / Lin, J. / De Maria, L. / Wogulis, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ha5.cif.gz | 108.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ha5.ent.gz | 82.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ha5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ha5_validation.pdf.gz | 450.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ha5_full_validation.pdf.gz | 454.6 KB | Display | |
Data in XML | 6ha5_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 6ha5_validation.cif.gz | 33.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/6ha5 ftp://data.pdbj.org/pub/pdb/validation_reports/ha/6ha5 | HTTPS FTP |
-Related structure data
Related structure data | 6h1zC 6haqC 3zudS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: HIC / Beg label comp-ID: HIC / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 1 - 228 / Label seq-ID: 1 - 228
|
-Components
#1: Protein | Mass: 24239.771 Da / Num. of mol.: 2 / Mutation: L90V/D131S/M134L/A141W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neosartorya fumigata (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_4G07850 / Production host: Aspergillus oryzae (mold) References: UniProt: Q4WP32, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds #2: Chemical | #3: Chemical | ChemComp-ACT / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.21 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: reservoir consisting of 0.1 M cobalt chloride, 0.1 M Tris pH 8.5; 20 %w/v Polyvinylpyrrolidone K15 and a 1:1 protein reservoir ratio in 0.3 microliter drop Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03982 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 25, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03982 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→20 Å / Num. obs: 27929 / % possible obs: 96.4 % / Redundancy: 3.9 % / Rsym value: 0.063 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.87→1.92 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 6.4 / Rsym value: 0.25 / % possible all: 95 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZUD Resolution: 1.87→19.37 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.049 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.133 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.89 Å2 / Biso mean: 21.613 Å2 / Biso min: 10.96 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.87→19.37 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Ens-ID: 1 / Number: 7287 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.87→1.918 Å / Total num. of bins used: 20
|