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- PDB-7nim: X-ray crystal structure of LsAA9A - cinnamon extract soak -

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Basic information

Entry
Database: PDB / ID: 7nim
TitleX-ray crystal structure of LsAA9A - cinnamon extract soak
ComponentsAuxiliary activity 9
KeywordsOXIDOREDUCTASE / Enzyme / Complex / Inhibitor
Function / homology
Function and homology information


lytic cellulose monooxygenase (C4-dehydrogenating) / cellulose catabolic process / monooxygenase activity / extracellular region / metal ion binding
Similarity search - Function
Auxiliary Activity family 9 / : / Auxiliary Activity family 9 (formerly GH61)
Similarity search - Domain/homology
ACETATE ION / COPPER (II) ION / Cinnamtannin B1 / Chem-UFN / AA9 family lytic polysaccharide monooxygenase A
Similarity search - Component
Biological speciesLentinus similis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsFrandsen, K.E.H. / Tokin, R. / Skov, L. / Johansen, K.S. / Lo Leggio, L.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17SA0027704 Denmark
CitationJournal: New Phytol. / Year: 2021
Title: Inhibition of lytic polysaccharide monooxygenase by natural plant extracts.
Authors: Tokin, R. / Frandsen, K.E.H. / Ipsen, J.O. / Lo Leggio, L. / Poojary, M.M. / Berrin, J.G. / Grisel, S. / Brander, S. / Jensen, P.E. / Johansen, K.S.
History
DepositionFeb 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Auxiliary activity 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,49010
Polymers25,2731
Non-polymers2,2179
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-45 kcal/mol
Surface area10330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.179, 125.179, 125.179
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-679-

HOH

21A-761-

HOH

31A-773-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Auxiliary activity 9


Mass: 25272.850 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lentinus similis (fungus) / Production host: Aspergillus oryzae (mold) / References: UniProt: A0A0S2GKZ1
#3: 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

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Non-polymers , 6 types, 386 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-UFK / Cinnamtannin B1 / (1R,5R,6R,7S,13S,21R)-5,13-bis(3,4-dihydroxyphenyl)-7-[(2R,3R)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-3,4-dihydro-2H-chromen-8-yl]-4,12,14-trioxapentacyclo[11.7.1.02,11.03,8.015,20]henicosa-2(11),3(8),9,15,17,19-hexaene-6,9,17,19,21-pentol


Mass: 864.757 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H36O18 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-UFN / Modified form of Cinnamtannin B1 with sp3 hybridized C5' / Cca6


Mass: 866.772 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H38O18 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.23 Å3/Da / Density % sol: 61.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 3.5 M NaCl, 0.1 M citric acid pH 4.0. 20-25 mg/ml LsAA9A. 2 ul hanging drops (1:1 protein:reservoir ratio).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2019
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.45→44.3 Å / Num. obs: 59727 / % possible obs: 100 % / Redundancy: 70.1 % / CC1/2: 0.999 / Rrim(I) all: 0.165 / Net I/σ(I): 20.57
Reflection shellResolution: 1.45→1.54 Å / Redundancy: 41.3 % / Num. unique obs: 9464 / CC1/2: 0.71 / Rrim(I) all: 1.846 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5ACH

5ach


Resolution: 1.45→44.3 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.126 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 3009 5 %RANDOM
Rwork0.1672 ---
obs0.1683 56643 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.38 Å2 / Biso mean: 21.047 Å2 / Biso min: 12.05 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.45→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 148 395 2331
Biso mean--33.16 35.78 -
Num. residues----235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0132057
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181738
X-RAY DIFFRACTIONr_angle_refined_deg2.0831.7472877
X-RAY DIFFRACTIONr_angle_other_deg1.5841.6294013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8515248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.53523.58792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.6115246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.84157
X-RAY DIFFRACTIONr_chiral_restr0.1330.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022381
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02468
LS refinement shellResolution: 1.45→1.538 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.416 456 -
Rwork0.406 9022 -
all-9478 -
obs--100 %

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