+Open data
-Basic information
Entry | Database: PDB / ID: 7ze9 | |||||||||
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Title | Structure of an AA16 LPMO-like protein | |||||||||
Components | Chitin-binding type-4 domain-containing protein | |||||||||
Keywords | METAL BINDING PROTEIN / Carbohydrate Active Enzyme / Auxillary Activity / LPMO / AA16 | |||||||||
Function / homology | Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / ACETATE ION / COPPER (II) ION / Chitin-binding type-4 domain-containing protein Function and homology information | |||||||||
Biological species | Thermothelomyces thermophilus (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.646 Å | |||||||||
Authors | Huang, Z. / Banerjee, S. / Muderspach, S.J. / Sun, P. / van Berkel, W.J.H. / Kabel, M.A. / Lo Leggio, L. | |||||||||
Funding support | Denmark, 2items
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Citation | Journal: Acs Catalysis / Year: 2023 Title: AA16 Oxidoreductases Boost Cellulose-Active AA9 Lytic Polysaccharide Monooxygenases from Myceliophthora thermophila. Authors: Sun, P. / Huang, Z. / Banerjee, S. / Kadowaki, M.A.S. / Veersma, R.J. / Magri, S. / Hilgers, R. / Muderspach, S.J. / Laurent, C.V.F.P. / Ludwig, R. / Cannella, D. / Lo Leggio, L. / van ...Authors: Sun, P. / Huang, Z. / Banerjee, S. / Kadowaki, M.A.S. / Veersma, R.J. / Magri, S. / Hilgers, R. / Muderspach, S.J. / Laurent, C.V.F.P. / Ludwig, R. / Cannella, D. / Lo Leggio, L. / van Berkel, W.J.H. / Kabel, M.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ze9.cif.gz | 126.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ze9.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ze9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ze9_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 7ze9_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 7ze9_validation.xml.gz | 23 KB | Display | |
Data in CIF | 7ze9_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/7ze9 ftp://data.pdbj.org/pub/pdb/validation_reports/ze/7ze9 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain: (Details: Chains AAA BBB CCC) |
-Components
-Protein , 1 types, 3 molecules AAABBBCCC
#1: Protein | Mass: 20510.879 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermothelomyces thermophilus (fungus) / Strain: ATCC 42464 / BCRC 31852 / DSM 1799 / Gene: MYCTH_2306267 / Production host: Thermothelomyces thermophilus (fungus) / References: UniProt: G2QH80 |
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-Sugars , 3 types, 6 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source #4: Sugar | |
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-Non-polymers , 3 types, 155 molecules
#5: Chemical | #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.76 Å3/Da / Density % sol: 55.49 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M buffer system 1 (1 M MES/ 1M Imidazole, pH 6.5), 45% EDO_P8K (40% w/v Ethylene glycol, 20% w/v PEG 8000), divalent cations (0.3 M Magnesium Chloride, O.3 M Calcium Chloride) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 18, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.646→85.554 Å / Num. obs: 19765 / % possible obs: 99.1 % / Redundancy: 4 % / CC1/2: 0.99 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.65→2.69 Å / Num. unique obs: 978 / CC1/2: 0.76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Alphafold model Resolution: 2.646→85.554 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.173 / SU B: 11.827 / SU ML: 0.235 / Average fsc free: 0.9014 / Average fsc work: 0.9184 / Cross valid method: FREE R-VALUE / ESU R: 0.742 / ESU R Free: 0.3 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2.646→85.554 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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