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- PDB-8s3l: X-ray crystal structure of LsAA9A -

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Basic information

Entry
Database: PDB / ID: 8s3l
TitleX-ray crystal structure of LsAA9A
ComponentsEndo-beta-1,4-glucanase D
KeywordsOXIDOREDUCTASE / LPMO
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
beta-cellotetraose / COPPER (II) ION / AA9 family lytic polysaccharide monooxygenase A
Similarity search - Component
Biological speciesPanus similis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsFrandsen, K.E.H. / Di Domenico, V. / Lo Leggio, L.
Funding support Denmark, 5items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17SA0027704 Denmark
Novo Nordisk FoundationNNF21OC0071799 Denmark
Danish Council for Independent Research8021-00273B Denmark
The Carlsberg FoundationCF16-0673 Denmark
The Carlsberg FoundationCF17-0533 Denmark
CitationJournal: To Be Published
Title: X-ray crystal structure of LsAA9A
Authors: Frandsen, K.E.H. / Di Domenico, V. / Lo Leggio, L.
History
DepositionFeb 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-beta-1,4-glucanase D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2605
Polymers25,2731
Non-polymers9874
Water79344
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-8 kcal/mol
Surface area9470 Å2
Unit cell
Length a, b, c (Å)126.720, 126.720, 126.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Endo-beta-1,4-glucanase D / Endoglucanase D / Carboxymethylcellulase D / Cellulase D


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

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellotetraose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#5: 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 , 3 types, 46 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cu
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.35 Å3/Da / Density % sol: 63.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: Crystallized in 3.5M NaCl, 0.1M citrate buffer pH 3.5. Soaked in 50% (w/v) PEG 6000, BSA 0.8 mg/ml, 0.1M citrate buffer pH 3.5 (5 microliter drop for 3 hours)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 4, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.6→73.2 Å / Num. obs: 10394 / % possible obs: 92.7 % / Redundancy: 4.56 % / CC1/2: 0.993 / Rrim(I) all: 0.137 / Net I/σ(I): 8.08
Reflection shellResolution: 2.6→2.67 Å / Num. unique obs: 773 / CC1/2: 0.799 / Rrim(I) all: 0.571 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→73.2 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.915 / SU B: 11.739 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.507 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26217 573 5.5 %RANDOM
Rwork0.19504 ---
obs0.19867 9820 93.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.714 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.6→73.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 61 44 1893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.1210.0121965
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161712
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.6582704
X-RAY DIFFRACTIONr_angle_other_deg0.4061.5683964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5595246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.68857
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17210247
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.050.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022287
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02435
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6624.132957
X-RAY DIFFRACTIONr_mcbond_other2.6614.132957
X-RAY DIFFRACTIONr_mcangle_it4.167.4271200
X-RAY DIFFRACTIONr_mcangle_other4.1587.4331201
X-RAY DIFFRACTIONr_scbond_it2.4344.2994
X-RAY DIFFRACTIONr_scbond_other2.4324.2995
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8457.6891499
X-RAY DIFFRACTIONr_long_range_B_refined6.04139.272114
X-RAY DIFFRACTIONr_long_range_B_other6.05239.292107
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.604→2.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 51 -
Rwork0.358 722 -
obs--96.99 %

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