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Yorodumi- PDB-4d7v: The structure of the catalytic domain of NcLPMO9C from the filame... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4d7v | ||||||
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Title | The structure of the catalytic domain of NcLPMO9C from the filamentous fungus Neurospora crassa | ||||||
Components | ENDOGLUCANASE IICellulase | ||||||
Keywords | OXIDOREDUCTASE / CATALYTIC DOMAIN / HEMICELLULOSE ACTIVE / AA9 | ||||||
Function / homology | Function and homology information cellulose binding / carbohydrate metabolic process / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | NEUROSPORA CRASSA (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Borisova, A.S. / Isaksen, T. / Sandgren, M. / Sorlie, M. / Eijsink, V.G.H. / Dimarogona, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Structural and Functional Characterization of a Lytic Polysaccharide Monooxygenase with Broad Substrate Specificity Authors: Borisova, A.S. / Isaksen, T. / Dimarogona, M. / Kognole, A.A. / Mathiesen, G. / Varnai, A. / Rohr, A.K. / Payne, C. / Sorlie, M. / Sandgren, M. / Eijsink, V.G.H. / Sorlie, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d7v.cif.gz | 103 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d7v.ent.gz | 83.3 KB | Display | PDB format |
PDBx/mmJSON format | 4d7v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/4d7v ftp://data.pdbj.org/pub/pdb/validation_reports/d7/4d7v | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23345.139 Da / Num. of mol.: 2 / Fragment: AA9, RESIDUES 17-243 Source method: isolated from a genetically manipulated source Details: CATALYTIC DOMAIN OF NCLPMO9C Source: (gene. exp.) NEUROSPORA CRASSA (STRAIN ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (fungus) Strain: ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987 Gene: GH61-3, NCU02916 / Plasmid: PPINK-GAPHC / Production host: PICHIA PASTORIS (fungus) / Strain (production host): PICHIAPINK STRAIN4 / References: UniProt: Q7SHI8 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ACT / #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | CATALYTIC DOMAIN OF FULL LENGTH ENZYME | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.4 % / Description: NONE |
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Crystal grow | pH: 8 / Details: 0.2M ZINC ACETATE, 17.5% PEG3350, pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→64.41 Å / Num. obs: 29831 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 7.5 Å2 / Rmerge(I) obs: 0.31 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.27 / Mean I/σ(I) obs: 2 / % possible all: 98.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: SAME PROTEIN WITH ONE METAL INSTEAD OF 3 Resolution: 1.9→64.406 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.906 / SU B: 5.829 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 182-184 HAVE BEEN OMITTED IN CHAINB DUE TO INSUFFICIENT ELECTRON DENSITY
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.993 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→64.406 Å
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Refine LS restraints |
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