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Yorodumi- PDB-7t5d: Neutron structure of Neurospora crassa Lytic Polysaccharide Monoo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7t5d | ||||||||||||
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Title | Neutron structure of Neurospora crassa Lytic Polysaccharide Monooxygenase 9D (NcLPMO9D) ascorbate soak | ||||||||||||
Components | Lytic polysaccharide monooxygenase | ||||||||||||
Keywords | OXIDOREDUCTASE / LPMO / monooxygenase / PMO / metalloproteins / copper | ||||||||||||
Function / homology | Function and homology information monooxygenase activity / hydrolase activity / extracellular region / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Neurospora crassa (fungus) | ||||||||||||
Method | NEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||||||||
Authors | Schroder, G.C. / Meilleur, F. | ||||||||||||
Funding support | South Africa, 3items
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Citation | Journal: Chem Sci / Year: 2022 Title: Capture of activated dioxygen intermediates at the copper-active site of a lytic polysaccharide monooxygenase. Authors: Schroder, G.C. / O'Dell, W.B. / Webb, S.P. / Agarwal, P.K. / Meilleur, F. #1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2021 Title: Preliminary results of neutron and X-ray diffraction data collection on a lytic polysaccharide monooxygenase under reduced and acidic conditions. Authors: Schroder, G.C. / O'Dell, W.B. / Swartz, P.D. / Meilleur, F. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7t5d.cif.gz | 193.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t5d.ent.gz | 154.1 KB | Display | PDB format |
PDBx/mmJSON format | 7t5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/7t5d ftp://data.pdbj.org/pub/pdb/validation_reports/t5/7t5d | HTTPS FTP |
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-Related structure data
Related structure data | 7t5cC 7t5eC 5tkhS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 23299.104 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neurospora crassa (fungus) / Gene: G15G9.090, GE21DRAFT_7469 / Production host: Komagataella pastoris (fungus) / Strain (production host): Superman5 / References: UniProt: Q8WZQ2 #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 417 molecules
#3: Chemical | #4: Chemical | ChemComp-PEO / | #5: Chemical | ChemComp-OXY / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: NEUTRON DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.3 % / Description: Crystals form rectangular shapes. |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 6 / Details: PEG 3350, HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||
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Diffraction source | Source: SPALLATION SOURCE / Site: ORNL Spallation Neutron Source / Beamline: MANDI / Wavelength: 2.0-4.0 | |||||||||
Detector | Type: ORNL ANGER CAMERA / Detector: DIFFRACTOMETER / Date: Nov 15, 2018 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→14.791 Å / Num. obs: 14168 / % possible obs: 91.16 % / Redundancy: 3.2 % / Biso Wilson estimate: 31.17 Å2 / CC1/2: 0.956 / Rmerge(I) obs: 0.1851 / Rrim(I) all: 0.2148 / Net I/σ(I): 7.15 | |||||||||
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.2737 / Mean I/σ(I) obs: 2.28 / Num. unique obs: 1300 / CC1/2: 0.297 / Rrim(I) all: 0.3327 / % possible all: 84.86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TKH Resolution: 2.4→14.791 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 2.34 / Phase error: 31.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.48 Å2 / Biso mean: 38.9543 Å2 / Biso min: 21.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→14.79 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: NEUTRON DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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