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- PDB-6yge: NADase from Aspergillus fumigatus -

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Basic information

Entry
Database: PDB / ID: 6yge
TitleNADase from Aspergillus fumigatus
ComponentsAfNADase
KeywordsHYDROLASE / NAD+ glycohydrolase / NAD / Ca-binding / homodimer / glycoprotein
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
ACETATE ION / Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 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 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)58,01412
Polymers55,3602
Non-polymers2,65410
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7780 Å2
ΔGint-11 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.788, 63.788, 257.995
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 , 3 types, 6 molecules

#2: 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
#3: 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
#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.: 3
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 , 3 types, 480 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.6→86 Å / Num. obs: 75947 / % possible obs: 92.77 % / Redundancy: 8.9 % / Biso Wilson estimate: 29.48 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.05886 / Net I/σ(I): 16.49
Reflection shellResolution: 1.6→1.657 Å / Rmerge(I) obs: 1.688 / Mean I/σ(I) obs: 0.71 / Num. unique obs: 7267 / CC1/2: 0.386

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Processing

Software
NameVersionClassification
XDSdata processing
Aimlessdata scaling
AutoSolphasing
PHASERphasing
PHENIX1.17.1-3660refinement
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.6→86 Å / SU ML: 0.2178 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4487
RfactorNum. reflection% reflection
Rfree0.2112 3780 4.98 %
Rwork0.1777 --
obs0.1793 75885 92.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.81 Å2
Refinement stepCycle: LAST / Resolution: 1.6→86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3285 0 171 476 3932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663607
X-RAY DIFFRACTIONf_angle_d0.88234949
X-RAY DIFFRACTIONf_chiral_restr0.0562551
X-RAY DIFFRACTIONf_plane_restr0.0068646
X-RAY DIFFRACTIONf_dihedral_angle_d9.6041568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.37291300.35212515X-RAY DIFFRACTION89.54
1.62-1.640.35311450.32982585X-RAY DIFFRACTION90.76
1.64-1.660.35061100.3182580X-RAY DIFFRACTION91.5
1.66-1.690.39171180.30082642X-RAY DIFFRACTION91.79
1.69-1.710.31241450.27772643X-RAY DIFFRACTION93.28
1.71-1.740.2651160.26222654X-RAY DIFFRACTION93.14
1.74-1.770.21111350.24662697X-RAY DIFFRACTION94.68
1.77-1.80.28731400.23352700X-RAY DIFFRACTION95.43
1.8-1.830.30941610.24292715X-RAY DIFFRACTION95.77
1.83-1.870.281740.24212737X-RAY DIFFRACTION96.74
1.87-1.90.24631420.22462774X-RAY DIFFRACTION98.02
1.9-1.950.2691960.21531629X-RAY DIFFRACTION57.35
1.95-1.990.25871680.2012822X-RAY DIFFRACTION99.34
1.99-2.040.24411440.19412842X-RAY DIFFRACTION99.73
2.04-2.10.2754970.20111911X-RAY DIFFRACTION67.13
2.1-2.160.22651560.18212867X-RAY DIFFRACTION99.9
2.16-2.230.26281500.1852862X-RAY DIFFRACTION99.83
2.23-2.310.2043820.18082208X-RAY DIFFRACTION75.65
2.31-2.40.22141770.18262852X-RAY DIFFRACTION99.93
2.4-2.510.22041200.18762911X-RAY DIFFRACTION99.93
2.51-2.640.2621600.18442886X-RAY DIFFRACTION100
2.64-2.810.22261440.17962495X-RAY DIFFRACTION86.7
2.81-3.020.22261470.17992919X-RAY DIFFRACTION99.97
3.02-3.330.19631570.17262926X-RAY DIFFRACTION99.87
3.33-3.810.19391370.15592567X-RAY DIFFRACTION87.76
3.81-4.80.15651590.13233012X-RAY DIFFRACTION100
4.8-860.17591700.17053154X-RAY DIFFRACTION99.64
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)
11.511259094840.158686015549-0.6882363234451.19801597723-0.3192891683692.221455172890.0707409857826-0.1313931157330.126493497690.1355880960.0360989672350.00624331342112-0.2657020657760.144885945961-0.1116757464560.261643038538-0.0466692980265-0.02043201901670.236902399522-0.002334201279670.20380120627321.107538265985.2766888749287.440416874
20.9049915567590.237021443909-0.1328758349041.3209164337-0.4374804008772.09545822745-0.02824601091320.10190548513-0.0623015984481-0.2545413064870.1600564964820.2450858873390.212754491353-0.207875458814-0.1246384449080.28175402991-0.082903983605-0.05049357991810.2020210125610.01134515672710.23754012359612.011312545773.8392016992269.843599195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'B' and resid 27 through 234)
2X-RAY DIFFRACTION2(chain 'A' and resid 26 through 233)

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