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- PDB-6ygf: NADase from Aspergillus fumigatus with trapped reaction products -

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Basic information

Entry
Database: PDB / ID: 6ygf
TitleNADase from Aspergillus fumigatus with trapped reaction products
ComponentsAfNADase
KeywordsHYDROLASE / NAD+ glycohydrolase / NAD / Ca-binding / homodimer / glycoprotein / nicotinamide / adenosine diphosphate ribose
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-AR6 / NICOTINAMIDE / PHOSPHATE ION / Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.3Nov 13, 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
B: AfNADase
A: AfNADase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,40716
Polymers55,3602
Non-polymers4,04714
Water10,070559
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9380 Å2
ΔGint3 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.815, 63.815, 257.723
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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Protein , 1 types, 2 molecules BA

#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 , 4 types, 6 molecules

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


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
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
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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.: 1
Source method: isolated from a genetically manipulated source
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
#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.: 2
Source method: isolated from a genetically manipulated source
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 , 5 types, 567 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#8: Chemical ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.9 Å3/Da / Density % sol: 57.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.04 M Potassium phosphate monobasic, 16% PEG 8000 and 20% glycerol

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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-F / Detector: PIXEL / Date: Oct 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.7→85.9 Å / Num. obs: 68236 / % possible obs: 99.74 % / Redundancy: 2 % / Biso Wilson estimate: 27.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02465 / Net I/σ(I): 15.17
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 1.04 / Num. unique obs: 6579 / CC1/2: 0.477

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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: 1.7→85.9 Å / SU ML: 0.2258 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.8257
RfactorNum. reflection% reflection
Rfree0.2013 3387 4.96 %
Rwork0.1692 --
obs0.1708 68230 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.24 Å2
Refinement stepCycle: LAST / Resolution: 1.7→85.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3302 0 263 559 4124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00683725
X-RAY DIFFRACTIONf_angle_d0.88055116
X-RAY DIFFRACTIONf_chiral_restr0.0553574
X-RAY DIFFRACTIONf_plane_restr0.0067653
X-RAY DIFFRACTIONf_dihedral_angle_d17.95061392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.4041390.38682604X-RAY DIFFRACTION96.14
1.72-1.750.35811250.33952575X-RAY DIFFRACTION98.65
1.75-1.780.29261390.29192677X-RAY DIFFRACTION100
1.78-1.810.25761190.25432678X-RAY DIFFRACTION100
1.81-1.840.27931600.23922644X-RAY DIFFRACTION100
1.84-1.870.28951070.22772724X-RAY DIFFRACTION100
1.87-1.910.24191390.21112651X-RAY DIFFRACTION100
1.91-1.950.22771500.19532645X-RAY DIFFRACTION99.96
1.95-1.990.21391530.1992702X-RAY DIFFRACTION100
1.99-2.030.26541460.2072627X-RAY DIFFRACTION99.96
2.03-2.090.23321370.19292710X-RAY DIFFRACTION99.93
2.09-2.140.2211230.18252685X-RAY DIFFRACTION100
2.14-2.20.22231330.17252716X-RAY DIFFRACTION100
2.2-2.280.23341300.16612687X-RAY DIFFRACTION100
2.28-2.360.21941540.16932690X-RAY DIFFRACTION100
2.36-2.450.22371510.16282701X-RAY DIFFRACTION100
2.45-2.560.19751680.1662672X-RAY DIFFRACTION100
2.56-2.70.19121270.15612707X-RAY DIFFRACTION100
2.7-2.870.19951460.16292719X-RAY DIFFRACTION100
2.87-3.090.17851410.1612745X-RAY DIFFRACTION99.97
3.09-3.40.17971650.15152708X-RAY DIFFRACTION99.97
3.4-3.890.16121680.14712746X-RAY DIFFRACTION100
3.89-4.90.15781250.12932851X-RAY DIFFRACTION99.93
4.9-42.950.21031420.17682979X-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)
11.220146059020.258687840256-0.6031384160581.09451173983-0.04711920388892.741105243480.0671414032195-0.121378106720.201478090455-0.02436174743220.0975410172398-0.0148329013908-0.200850309990.145538496254-0.1588116788830.127635536066-0.0381228641019-0.008389861228930.175913588503-0.02870502353460.204363844535-11.732604888630.169456526329.4938566532
20.7757884364470.3754511153640.02562230817961.21192211176-0.4857490776972.1925091658-0.06269950031390.1094595704810.0022760938247-0.3269357062030.2412515298150.2038689075980.220171971492-0.258797202247-0.1658748892190.253194349612-0.0942498974407-0.04428616772160.1934704883210.02368488030680.236475952264-20.188172271918.809395597711.6846320076
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid 26 through 234)
2X-RAY DIFFRACTION2(chain 'A' and resid 25 through 233)

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