+Open data
-Basic information
Entry | Database: PDB / ID: 7pqr | |||||||||
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Title | LsAA9A expressed in E. coli | |||||||||
Components | Auxiliary activity 9 | |||||||||
Keywords | OXIDOREDUCTASE / Copper binding protein / Beta-sandwich fold / Auxillary | |||||||||
Function / homology | Function and homology information cellulose binding / cellulase / cellulase activity / cellulose catabolic process / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | Lentinus similis (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å | |||||||||
Authors | Muderspach, S.J. / Metherall, J. / Ipsen, J. / Rollan, C.H. / Norholm, M. / Johansen, K.S. / Lo Leggio, L. | |||||||||
Funding support | Denmark, 2items
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Citation | Journal: Iucrj / Year: 2022 Title: Changes in active-site geometry on X-ray photoreduction of a lytic polysaccharide monooxygenase active-site copper and saccharide binding. Authors: Tandrup, T. / Muderspach, S.J. / Banerjee, S. / Santoni, G. / Ipsen, J.O. / Hernandez-Rollan, C. / Norholm, M.H.H. / Johansen, K.S. / Meilleur, F. / Lo Leggio, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pqr.cif.gz | 73.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pqr.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 7pqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/7pqr ftp://data.pdbj.org/pub/pdb/validation_reports/pq/7pqr | HTTPS FTP |
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-Related structure data
Related structure data | 7pxiC 7pxjC 7pxkC 7pxlC 7pxmC 7pxnC 7pxrC 7pxsC 7pxtC 7pxuC 7pxvC 7pxwC 7pydC 7pyeC 7pyfC 7pygC 7pyhC 7pyiC 7pylC 7pymC 7pynC 7pyoC 7pypC 7pyqC 7pyuC 7pywC 7pyxC 7pyyC 7pyzC 7pz0C 7pz3C 7pz4C 7pz5C 7pz6C 7pz7C 7pz8C 5achS S: Starting model for refinement C: citing same article (ref.) |
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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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25259.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lentinus similis (fungus) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0S2GKZ1 |
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-Non-polymers , 5 types, 455 molecules
#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-CU / | #4: Chemical | ChemComp-CL / #5: Chemical | #6: 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: 2.6 Å3/Da / Density % sol: 52.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 0.1 M sodium acetate pH 4.5, 1.8 M ammonium sulphate. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1.12713 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12713 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→48.92 Å / Num. obs: 63029 / % possible obs: 99.4 % / Redundancy: 6.14 % / CC1/2: 0.999 / Rrim(I) all: 0.077 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.3→1.33 Å / Redundancy: 3.06 % / Mean I/σ(I) obs: 1.09 / Num. unique obs: 8661 / CC1/2: 0.482 / Rrim(I) all: 1.25 / % possible all: 93.3 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ACH Resolution: 1.3→48.92 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.981 / WRfactor Rfree: 0.1544 / WRfactor Rwork: 0.1311 / FOM work R set: 0.8694 / SU B: 0.777 / SU ML: 0.031 / SU R Cruickshank DPI: 0.0384 / SU Rfree: 0.0405 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.038 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.62 Å2 / Biso mean: 17.567 Å2 / Biso min: 10.85 Å2
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Refinement step | Cycle: final / Resolution: 1.3→48.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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