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Yorodumi- PDB-7t5e: Neutron structure of Neurospora crassa Polysaccharide Monooxygena... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7t5e | ||||||||||||
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Title | Neutron structure of Neurospora crassa Polysaccharide Monooxygenase 9D (NcLPMO9D) low pH vapor exchange | ||||||||||||
Components | Lytic polysaccharide monooxygenase | ||||||||||||
Keywords | OXIDOREDUCTASE / LPMO / monooxygenase / PMO / metalloproteins | ||||||||||||
Function / homology | : / Auxiliary Activity family 9 / Auxiliary Activity family 9 (formerly GH61) / monooxygenase activity / hydrolase activity / extracellular region / COPPER (II) ION / Related to cel1 protein Function and homology information | ||||||||||||
Biological species | Neurospora crassa (fungus) | ||||||||||||
Method | X-RAY DIFFRACTION / NEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||||||||
Authors | Schroder, G.C. / Meilleur, F. | ||||||||||||
Funding support | United States, 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 | 7t5e.cif.gz | 210.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7t5e.ent.gz | 172.1 KB | Display | PDB format |
PDBx/mmJSON format | 7t5e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7t5e_validation.pdf.gz | 537.6 KB | Display | wwPDB validaton report |
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Full document | 7t5e_full_validation.pdf.gz | 538.2 KB | Display | |
Data in XML | 7t5e_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 7t5e_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/7t5e ftp://data.pdbj.org/pub/pdb/validation_reports/t5/7t5e | HTTPS FTP |
-Related structure data
Related structure data | 7t5cC 7t5dC 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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2 |
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Unit cell |
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-Components
#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 | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.98 % / Description: Crystals form rectangular shapes. |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 4.4 / Details: PEG 3350, HEPES |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Biso Wilson estimate: 17.17 Å2 / Entry-ID: 7T5E
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Reflection shell |
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-Processing
Software |
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Refinement | SU ML: 0.18 / R Free selection details: Random selection / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 18.75 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 5TKH / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL
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Refinement step | Cycle: final / Resolution: 1.9→12.662 Å
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Refine LS restraints |
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LS refinement shell | Rfactor Rfree error: 0
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