+Open data
-Basic information
Entry | Database: PDB / ID: 6rs7 | ||||||||||||||||||||||||
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Title | X-ray crystal structure of LsAA9B (deglycosylated form) | ||||||||||||||||||||||||
Components | AA9 | ||||||||||||||||||||||||
Keywords | UNKNOWN FUNCTION / Fungal / family AA9 | ||||||||||||||||||||||||
Function / homology | Coagulation Factor XIII; Chain A, domain 1 - #70 / Coagulation Factor XIII; Chain A, domain 1 / Distorted Sandwich / Mainly Beta / alpha-D-mannopyranose / NITRATE ION / TRIETHYLENE GLYCOL Function and homology information | ||||||||||||||||||||||||
Biological species | Lentinus similis (fungus) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||||||||||||||||||||
Authors | Frandsen, K.E.H. / Tovborg, M. / Poulsen, J.C.N. / Johansen, K.S. / Lo Leggio, L. | ||||||||||||||||||||||||
Funding support | Denmark, France, 7items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Insights into an unusual Auxiliary Activity 9 family member lacking the histidine brace motif of lytic polysaccharide monooxygenases. Authors: Frandsen, K.E.H. / Tovborg, M. / Jorgensen, C.I. / Spodsberg, N. / Rosso, M.N. / Hemsworth, G.R. / Garman, E.F. / Grime, G.W. / Poulsen, J.N. / Batth, T.S. / Miyauchi, S. / Lipzen, A. / ...Authors: Frandsen, K.E.H. / Tovborg, M. / Jorgensen, C.I. / Spodsberg, N. / Rosso, M.N. / Hemsworth, G.R. / Garman, E.F. / Grime, G.W. / Poulsen, J.N. / Batth, T.S. / Miyauchi, S. / Lipzen, A. / Daum, C. / Grigoriev, I.V. / Johansen, K.S. / Henrissat, B. / Berrin, J.G. / 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 | 6rs7.cif.gz | 108.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rs7.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 6rs7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/6rs7 ftp://data.pdbj.org/pub/pdb/validation_reports/rs/6rs7 | HTTPS FTP |
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-Related structure data
Related structure data | 6rs6C 6rs8C 6rs9C 3ejaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 23318.902 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Ser25 is modelled as a phophoserine (pSer25). / Source: (gene. exp.) Lentinus similis (fungus) / Production host: Aspergillus oryzae (mold) |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Sugar | ChemComp-MAN / |
-Non-polymers , 5 types, 250 molecules
#4: Chemical | ChemComp-MPD / ( | ||||||
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#5: Chemical | #6: Chemical | ChemComp-NO3 / #7: Chemical | ChemComp-PGE / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 16%(w/v) MPD (racemic) 16%(w/v) PEG 1000 16%(w/v) PEG 3350 20 mM of Glutamate, Alanine, Glycine, Lysine, and Serine (some racemic). 30 mM of each of NaNO3; Na2HPO4; (NH4)2SO4 100 mM Imidazole/MES 0.1 M (pH6.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 11, 2014 Details: Collimating mirror , double-crystal monochromator (DCM), focusing mirror |
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: 1.6→20 Å / Num. obs: 27139 / % possible obs: 98.5 % / Redundancy: 5.81 % / CC1/2: 0.998 / Rrim(I) all: 0.084 / Net I/σ(I): 14.39 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 3.59 % / Mean I/σ(I) obs: 1.94 / Num. unique obs: 4106 / CC1/2: 0.766 / Rrim(I) all: 0.82 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3EJA Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.375 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.097 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.437 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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