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- PDB-8pmr: NADase from Aspergillus fumigatus with mutated calcium binding mo... -

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Basic information

Entry
Database: PDB / ID: 8pmr
TitleNADase from Aspergillus fumigatus with mutated calcium binding motif (D219A/E220A)
ComponentsConidial surface nicotinamide adenine dinucleotide glycohydrolase nadA
KeywordsHYDROLASE / NADase / NAD hydrolase / Ca-binding / homodimer / glycoprotein / extracellular / TNT domain
Function / homologyTuberculosis necrotizing toxin / Tuberculosis necrotizing toxin / : / NAD+ glycohydrolase / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / extracellular region / metal ion binding / DI(HYDROXYETHYL)ETHER / Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA
Function and homology information
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsKallio, J.P. / Ferrario, E. / Stromland, O. / Ziegler, M.
Funding support Norway, 1items
OrganizationGrant numberCountry
Norwegian Research Council302314 Norway
CitationJournal: Biochemistry / Year: 2023
Title: Novel Calcium-Binding Motif Stabilizes and Increases the Activity of Aspergillus fumigatus Ecto-NADase.
Authors: Ferrario, E. / Kallio, J.P. / Stromland, O. / Ziegler, M.
History
DepositionJun 29, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA
B: Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA
C: Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA
D: Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,40123
Polymers110,3124
Non-polymers6,08919
Water10,935607
1
A: Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA
B: Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,55410
Polymers55,1562
Non-polymers3,3988
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint23 kcal/mol
Surface area20040 Å2
MethodPISA
2
C: Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA
D: Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,84713
Polymers55,1562
Non-polymers2,69111
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint4 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.897, 65.897, 488.199
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA / NADase / NAD(+) hydrolase nadA / NADP(+) hydrolase nadA


Mass: 27578.047 Da / Num. of mol.: 4 / Mutation: D219A/E220A
Source method: isolated from a genetically manipulated source
Details: MIFTNAILVISALLPATVLS = signal sequence D219A/E220A mutation from the original sequence AfNADase sequence DVLFQGPGHHHHHH= 3c protease site and His-tag
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Gene: nadA, AFUA_6G14470 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q4WL81, NAD+ glycohydrolase, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

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Sugars , 6 types, 11 molecules

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


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...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: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#6: 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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#8: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / 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 , 5 types, 615 molecules

#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#9: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C3H8O3
#10: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#11: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 607 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.77 Å3/Da / Density % sol: 55.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6 / Details: NaCl, MES, PEG 6000

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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: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.94→39.32 Å / Num. obs: 85149 / % possible obs: 96.35 % / Redundancy: 11.6 % / Biso Wilson estimate: 39.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0759 / Rpim(I) all: 0.02293 / Net I/σ(I): 18.85
Reflection shellResolution: 1.94→2.012 Å / Rmerge(I) obs: 2.11 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 6421 / CC1/2: 0.275 / Rpim(I) all: 0.885

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→39.32 Å / SU ML: 0.2765 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3932
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2157 4211 4.99 %
Rwork0.1821 80229 -
obs0.1838 84440 96.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.38 Å2
Refinement stepCycle: LAST / Resolution: 1.94→39.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6588 0 400 607 7595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00967220
X-RAY DIFFRACTIONf_angle_d1.1069891
X-RAY DIFFRACTIONf_chiral_restr0.06241109
X-RAY DIFFRACTIONf_plane_restr0.00961270
X-RAY DIFFRACTIONf_dihedral_angle_d13.72332695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.960.4138670.38481010X-RAY DIFFRACTION37.25
1.96-1.990.4448960.39072088X-RAY DIFFRACTION74.64
1.99-2.010.34731460.34182451X-RAY DIFFRACTION89.58
2.01-2.040.3141360.28212697X-RAY DIFFRACTION96.76
2.04-2.060.27541310.25282767X-RAY DIFFRACTION98.37
2.06-2.090.27581040.23392723X-RAY DIFFRACTION99.09
2.09-2.120.26611340.2322863X-RAY DIFFRACTION99.57
2.12-2.150.27151700.22632693X-RAY DIFFRACTION99.72
2.15-2.190.29251430.21612777X-RAY DIFFRACTION99.62
2.19-2.220.27531450.21142729X-RAY DIFFRACTION99.38
2.22-2.260.21861440.20762829X-RAY DIFFRACTION99.77
2.26-2.30.26011510.20292683X-RAY DIFFRACTION99.61
2.3-2.350.25371350.20162826X-RAY DIFFRACTION99.7
2.35-2.40.25471560.20862710X-RAY DIFFRACTION99.86
2.4-2.450.21821610.1962801X-RAY DIFFRACTION99.7
2.45-2.50.25241580.19562700X-RAY DIFFRACTION99.37
2.5-2.570.28681620.20212757X-RAY DIFFRACTION100
2.57-2.640.24661560.20142830X-RAY DIFFRACTION99.77
2.64-2.710.21721420.18832716X-RAY DIFFRACTION99.69
2.71-2.80.22761320.19412761X-RAY DIFFRACTION99.69
2.8-2.90.25791530.19282784X-RAY DIFFRACTION99.83
2.9-3.020.23481450.20392789X-RAY DIFFRACTION99.93
3.02-3.160.21351410.20242788X-RAY DIFFRACTION99.97
3.16-3.320.19771380.19082758X-RAY DIFFRACTION100
3.32-3.530.23081290.17822781X-RAY DIFFRACTION100
3.53-3.80.21341500.16712785X-RAY DIFFRACTION100
3.8-4.180.1691780.14452743X-RAY DIFFRACTION100
4.18-4.790.1551390.13272790X-RAY DIFFRACTION99.97
4.79-6.030.19531270.15692826X-RAY DIFFRACTION100
6.03-39.320.20051420.18272774X-RAY DIFFRACTION99.86
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)
11.32105806465-0.0342689689135-0.9988490593650.756540305617-0.09145860131082.390006769530.145976028045-0.1194225826170.21212345011-0.0104320727839-0.002252475662480.0137982031496-0.3714353033260.228771891868-0.1217373628370.44600144695-0.1447331702410.02637777193630.280898500944-0.0524041410840.312022744249.5207245683119.3614086596-2.86068017871
21.21447011547-0.1816813410560.1666051459970.769032580814-0.2067769333863.627732682030.02494180780420.0916942744045-0.0439903153988-0.1304852635240.01648649095210.05708127540230.0771887523532-0.0366708946893-0.04192666807850.423133371243-0.07869199097580.0370972948350.225768893752-0.04799457578650.2855442704045.967452897843.72801749648-21.4636274119
31.204644297750.232854461789-0.01996748611011.620942122950.9202927950752.97637110719-0.07188414983040.06449068746280.0335843371782-0.1889626404930.161397457094-0.119289887966-0.01943843925330.258216715906-0.08205464902650.308082591189-0.1022393366740.01939456208170.300061666201-0.02646674592990.273946349068-10.671575422-7.7361498692518.5735919846
40.824667929439-0.03337991007180.9164759238671.494280673120.1591848213292.907776144150.083271649701-0.174436673199-0.1509029674140.0275144286442-0.02180331708910.2884661525140.428227799422-0.270643529313-0.05936691429470.348773354839-0.1111527792010.05116932523640.413186748298-0.04148275312790.378311449543-23.33960638-17.313702811736.8035923092
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11(chain 'A' and resid 23 through 600)AA23 - 600
22(chain 'B' and resid 25 through 600)BB25 - 600
33(chain 'C' and resid 23 through 700)CC23 - 700
44(chain 'D' and resid 24 through 502)DD24 - 502

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