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- PDB-7p3u: Chitin-active fungal AA11 LPMO -

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Basic information

Entry
Database: PDB / ID: 7p3u
TitleChitin-active fungal AA11 LPMO
ComponentsEndoglucanase, putative
KeywordsOXIDOREDUCTASE / LPMO / AA11 / AfAA11A / Chitin
Function / homologyOxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; Miscellaneous / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / hydrolase activity, acting on glycosyl bonds / chitin catabolic process / polysaccharide catabolic process / metal ion binding / AA11 family lytic polysaccharide monooxygenase A
Function and homology information
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRohr, A.K. / Stoepamo, F.G. / Eijsink, V.G.H.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway243663 Norway
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Characterization of a lytic polysaccharide monooxygenase from Aspergillus fumigatus shows functional variation among family AA11 fungal LPMOs.
Authors: Stopamo, F.G. / Rohr, A.K. / Mekasha, S. / Petrovic, D.M. / Varnai, A. / Eijsink, V.G.H.
History
DepositionJul 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9842
Polymers21,7631
Non-polymers2211
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint4 kcal/mol
Surface area8870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.986, 47.283, 115.588
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Endoglucanase, putative


Mass: 21763.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain CEA10 / CBS 144.89 / FGSC A1163) (mold)
Strain: CEA10 / CBS 144.89 / FGSC A1163 / Gene: AFUB_044010 / Production host: Komagataella pastoris (fungus) / References: UniProt: B0XZD3
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 0.1 M bicine (pH 9.0) and 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.946444 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.946444 Å / Relative weight: 1
ReflectionResolution: 1.5→47.28 Å / Num. obs: 36807 / % possible obs: 99.8 % / Redundancy: 12.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Net I/σ(I): 19.2
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.361 / Num. unique obs: 1849 / CC1/2: 0.986

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MAH

4mah


Resolution: 1.5→29.886 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.661 / SU ML: 0.057 / Cross valid method: FREE R-VALUE / ESU R: 0.067 / ESU R Free: 0.067
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1974 1959 5.332 %
Rwork0.1464 34779 -
all0.149 --
obs-36738 99.677 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.943 Å2
Baniso -1Baniso -2Baniso -3
1-4.348 Å2-0 Å20 Å2
2---1.644 Å2-0 Å2
3----2.703 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1527 0 14 182 1723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131596
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171381
X-RAY DIFFRACTIONr_angle_refined_deg1.8271.6642184
X-RAY DIFFRACTIONr_angle_other_deg1.4891.5833201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2485202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.37323.81676
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35915223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.047155
X-RAY DIFFRACTIONr_chiral_restr0.0950.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021866
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02374
X-RAY DIFFRACTIONr_nbd_refined0.2560.2258
X-RAY DIFFRACTIONr_symmetry_nbd_other0.230.21291
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2781
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1170.2709
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2115
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1430.26
X-RAY DIFFRACTIONr_nbd_other0.1890.223
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0830.27
X-RAY DIFFRACTIONr_mcbond_it3.42.766805
X-RAY DIFFRACTIONr_mcbond_other3.222.76804
X-RAY DIFFRACTIONr_mcangle_it3.5164.1671005
X-RAY DIFFRACTIONr_mcangle_other3.5774.1731006
X-RAY DIFFRACTIONr_scbond_it5.13.187791
X-RAY DIFFRACTIONr_scbond_other5.0973.188792
X-RAY DIFFRACTIONr_scangle_it5.64.6271178
X-RAY DIFFRACTIONr_scangle_other5.5974.6271179
X-RAY DIFFRACTIONr_lrange_it5.12434.0781740
X-RAY DIFFRACTIONr_lrange_other4.98933.641714
X-RAY DIFFRACTIONr_rigid_bond_restr4.27732977
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.3111660.2722523X-RAY DIFFRACTION99.8144
1.539-1.5810.2671380.2322482X-RAY DIFFRACTION100
1.581-1.6270.2261330.1732400X-RAY DIFFRACTION100
1.627-1.6770.2071430.162315X-RAY DIFFRACTION99.9593
1.677-1.7320.2381210.1422289X-RAY DIFFRACTION99.9585
1.732-1.7930.2111130.1342222X-RAY DIFFRACTION100
1.793-1.860.2061140.1272133X-RAY DIFFRACTION99.9555
1.86-1.9360.2281150.1312049X-RAY DIFFRACTION100
1.936-2.0220.1941130.1271962X-RAY DIFFRACTION100
2.022-2.1210.1891180.1291863X-RAY DIFFRACTION100
2.121-2.2360.202910.1321826X-RAY DIFFRACTION100
2.236-2.3710.198950.1231702X-RAY DIFFRACTION100
2.371-2.5350.204930.1311610X-RAY DIFFRACTION100
2.535-2.7380.192810.1321515X-RAY DIFFRACTION100
2.738-2.9990.183750.1491389X-RAY DIFFRACTION100
2.999-3.3530.195640.161262X-RAY DIFFRACTION100
3.353-3.8710.197640.1541148X-RAY DIFFRACTION99.7531
3.871-4.740.142530.122956X-RAY DIFFRACTION99.0186
4.74-6.6980.199450.153755X-RAY DIFFRACTION98.6436

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