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- PDB-8s3f: X-ray crystal structure of LsAA9A -

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Basic information

Entry
Database: PDB / ID: 8s3f
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
CITRIC ACID / COPPER (II) ION / TRIETHYLENE GLYCOL / AA9 family lytic polysaccharide monooxygenase A
Similarity search - Component
Biological speciesPanus similis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.76 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)26,3508
Polymers25,2731
Non-polymers1,0787
Water4,846269
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint3 kcal/mol
Surface area9640 Å2
Unit cell
Length a, b, c (Å)123.920, 123.920, 123.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-538-

HOH

21A-666-

HOH

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Components

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Protein / Sugars , 2 types, 2 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
#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 , 4 types, 275 molecules

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


Mass: 63.546 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cu
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 3.15 Å3/Da / Density % sol: 60.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: Crystallized in 3.8M NaCl, 0.1M citrate buffer pH 3.5. Soaked in 20% (w/v) PEG 6000, BSA 0.8 mg/ ml 75 mM Cellotetraose, 0.1M citrate buffer pH 3.5 (2 x 10 minutes).

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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: 1.76→71.65 Å / Num. obs: 32397 / % possible obs: 98.2 % / Redundancy: 4.38 % / CC1/2: 0.995 / Rrim(I) all: 0.118 / Net I/σ(I): 8.41
Reflection shellResolution: 1.76→1.8 Å / Redundancy: 4.47 % / Mean I/σ(I) obs: 2.31 / Num. unique obs: 2351 / CC1/2: 0.824 / Rrim(I) all: 0.557 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.76→71.65 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.872 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18717 1634 5 %RANDOM
Rwork0.15676 ---
obs0.15833 30762 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.006 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.76→71.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 68 269 2125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121964
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161754
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.6462703
X-RAY DIFFRACTIONr_angle_other_deg0.5291.5634054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0575251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.72257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.5710248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022323
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02439
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_it1.5461.726968
X-RAY DIFFRACTIONr_mcbond_other1.5461.726968
X-RAY DIFFRACTIONr_mcangle_it2.0173.0961216
X-RAY DIFFRACTIONr_mcangle_other2.0223.0961217
X-RAY DIFFRACTIONr_scbond_it2.3751.953996
X-RAY DIFFRACTIONr_scbond_other2.3741.956997
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1213.4551483
X-RAY DIFFRACTIONr_long_range_B_refined4.76219.842305
X-RAY DIFFRACTIONr_long_range_B_other4.45618.742227
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.802 Å
RfactorNum. reflection% reflection
Rfree0.299 126 -
Rwork0.258 2225 -
obs--98.78 %

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