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- PDB-6ygg: NADase from Aspergillus fumigatus complexed with a substrate anologue -

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Basic information

Entry
Database: PDB / ID: 6ygg
TitleNADase from Aspergillus fumigatus complexed with a substrate anologue
ComponentsAfNADase
KeywordsHYDROLASE / NAD+ glycohydrolase / NAD / Ca-binding / homodimer / glycoprotein / benzamide adenine dinucleotide
Function / homology
Function and homology information


NAD+ glycohydrolase / NADP+ nucleosidase activity / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / extracellular region / metal ion binding
Similarity search - Function
: / Tuberculosis necrotizing toxin / Tuberculosis necrotizing toxin
Similarity search - Domain/homology
Chem-DQV / Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsStromland, O. / Ziegler, M. / Kallio, J.P.
CitationJournal: Nat Commun / Year: 2021
Title: Discovery of fungal surface NADases predominantly present in pathogenic species.
Authors: Stromland, O. / Kallio, J.P. / Pschibul, A. / Skoge, R.H. / Hardardottir, H.M. / Sverkeli, L.J. / Heinekamp, T. / Kniemeyer, O. / Migaud, M. / Makarov, M.V. / Gossmann, T.I. / Brakhage, A.A. / Ziegler, M.
History
DepositionMar 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: 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
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 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: AfNADase
B: AfNADase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,99612
Polymers55,3602
Non-polymers3,63610
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-9 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.050, 64.318, 161.007
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein AfNADase


Mass: 27680.092 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Gene: AFUA_6G14470 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q4WL81

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Sugars , 3 types, 6 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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, 462 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#7: Chemical ChemComp-DQV / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5S)-5-(3-carbamoylphenyl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)


Mass: 662.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H28N6O14P2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate, 0.3 M CaCl2 and 20-25% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91589 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91589 Å / Relative weight: 1
ReflectionResolution: 1.85→48.66 Å / Num. obs: 45536 / % possible obs: 98.52 % / Redundancy: 6.7 % / Biso Wilson estimate: 25.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1426 / Net I/σ(I): 9.33
Reflection shellResolution: 1.85→1.916 Å / Rmerge(I) obs: 1.658 / Mean I/σ(I) obs: 0.95 / Num. unique obs: 4447 / CC1/2: 0.513

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata processing
Aimlessdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1292105770

Resolution: 1.85→48.66 Å / SU ML: 0.2293 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.7699
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2259 2313 5.08 %
Rwork0.1853 43195 -
obs0.1874 45508 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.7 Å2
Refinement stepCycle: LAST / Resolution: 1.85→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3302 0 237 458 3997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00763654
X-RAY DIFFRACTIONf_angle_d1.00125019
X-RAY DIFFRACTIONf_chiral_restr0.0677567
X-RAY DIFFRACTIONf_plane_restr0.0066643
X-RAY DIFFRACTIONf_dihedral_angle_d18.1081351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.38771320.37462478X-RAY DIFFRACTION97.06
1.89-1.930.34561150.3312477X-RAY DIFFRACTION98.07
1.93-1.970.3361290.28842507X-RAY DIFFRACTION98.21
1.97-2.020.34011510.26132461X-RAY DIFFRACTION97.54
2.02-2.080.25451440.23912469X-RAY DIFFRACTION97.54
2.08-2.140.28541550.222492X-RAY DIFFRACTION98.44
2.14-2.210.27921290.20482509X-RAY DIFFRACTION98.29
2.21-2.290.23151250.19642529X-RAY DIFFRACTION98.52
2.29-2.380.23711390.19022503X-RAY DIFFRACTION98.36
2.38-2.490.27841290.17992541X-RAY DIFFRACTION98.42
2.49-2.620.23431140.17722541X-RAY DIFFRACTION98.85
2.62-2.780.23281240.17632556X-RAY DIFFRACTION98.93
2.78-30.22711550.17742556X-RAY DIFFRACTION99.05
3-3.30.22491290.17052584X-RAY DIFFRACTION99.2
3.3-3.770.2211480.15982597X-RAY DIFFRACTION99.35
3.78-4.750.14561510.13532619X-RAY DIFFRACTION99.64
4.76-48.660.19261440.18312776X-RAY DIFFRACTION99.49
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0754139824964-0.01402549496170.1553359179280.5592764651280.01624752603430.2567133695540.0356625333488-0.00830400270322-0.0287723743485-0.06946164348650.04775980256590.07719799684120.0890795355710.0180652277776-1.79635616214E-90.137687650648-0.0020634021568-0.02764654390720.136588733978-0.0001906541091390.142257754789-23.0600431032-2.61750598881-28.7407623514
20.08396492330030.0384666051801-0.08736855695240.5007638626360.1992704993530.288010038899-0.01256137106510.004055152818590.02261470381330.08559232533880.04541416181410.0400787043649-0.0029332733071-0.00137103325021-2.0778096139E-90.1150621906180.0198024590587-0.005672097708140.142663103507-0.00156598749320.133621761085-19.313814228411.7792362811-11.8177291333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 26 through 234)
2X-RAY DIFFRACTION2(chain 'B' and resid 27 through 235)

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