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- PDB-8pms: NADase from Aspergillus fumigatus with replaced C-terminus from N... -

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Basic information

Entry
Database: PDB / ID: 8pms
TitleNADase from Aspergillus fumigatus with replaced C-terminus from Neurospora crassa
ComponentsConidial surface nicotinamide adenine dinucleotide glycohydrolase nadA
KeywordsHYDROLASE / NADase / NAD hydrolase / Ca-binding / homodimer / glycoprotein / extracellular
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
ACRYLIC ACID / Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
Revision 1.2Nov 6, 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: 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)111,52625
Polymers106,6054
Non-polymers4,92221
Water2,414134
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)56,62216
Polymers53,3022
Non-polymers3,31914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint14 kcal/mol
Surface area18660 Å2
MethodPISA
2
C: Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA
hetero molecules

D: Conidial surface nicotinamide adenine dinucleotide glycohydrolase nadA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9059
Polymers53,3022
Non-polymers1,6037
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y,x-1,-z1
Buried area4130 Å2
ΔGint-2 kcal/mol
Surface area18350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.018, 101.018, 366.335
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-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: 26651.146 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: MIFTNAILVISALLPATVLS = signal sequence EDPQRLVPRNYGT at the C-terminus is from N.crassa NADase, replacing the original C-terminus of AfNADase 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 , 4 types, 12 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.: 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
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam 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_c3-d1WURCSPDB2Glycan 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-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}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.: 9 / 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, 143 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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Chemical
ChemComp-AKR / ACRYLIC ACID


Mass: 72.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 4.38 Å3/Da / Density % sol: 71.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: MgCl2, HEPES and Polyacrylic acid 5100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03321 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.4→46.67 Å / Num. obs: 75255 / % possible obs: 99.81 % / Redundancy: 14.38 % / Biso Wilson estimate: 73.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08156 / Rpim(I) all: 0.02955 / Net I/σ(I): 14.38
Reflection shellResolution: 2.4→2.486 Å / Rmerge(I) obs: 2.137 / Num. unique obs: 7381 / CC1/2: 0.456 / Rpim(I) all: 0.7324

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→46.67 Å / SU ML: 0.4143 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.8452
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2242 3632 4.83 %
Rwork0.2036 71608 -
obs0.2046 75240 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.65 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5937 0 320 134 6391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916600
X-RAY DIFFRACTIONf_angle_d1.419043
X-RAY DIFFRACTIONf_chiral_restr0.0898994
X-RAY DIFFRACTIONf_plane_restr0.01351176
X-RAY DIFFRACTIONf_dihedral_angle_d13.14982442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.52581210.46812704X-RAY DIFFRACTION99.82
2.43-2.460.4561130.42722773X-RAY DIFFRACTION99.97
2.46-2.50.37881300.35652671X-RAY DIFFRACTION99.96
2.5-2.540.38131340.33882730X-RAY DIFFRACTION100
2.54-2.580.33971230.31282703X-RAY DIFFRACTION100
2.58-2.620.34151410.29542718X-RAY DIFFRACTION99.93
2.62-2.660.32281480.27632716X-RAY DIFFRACTION99.97
2.66-2.710.32071570.28162682X-RAY DIFFRACTION100
2.71-2.770.34871260.27792721X-RAY DIFFRACTION99.82
2.77-2.820.33421330.27442737X-RAY DIFFRACTION99.97
2.82-2.880.32391610.29282698X-RAY DIFFRACTION99.93
2.88-2.950.37041390.34632712X-RAY DIFFRACTION99.96
2.95-3.020.30461570.29672701X-RAY DIFFRACTION99.97
3.02-3.110.36451370.26362758X-RAY DIFFRACTION100
3.11-3.20.27511380.24392749X-RAY DIFFRACTION99.93
3.2-3.30.24681500.23672706X-RAY DIFFRACTION99.79
3.3-3.420.23691380.23282759X-RAY DIFFRACTION99.86
3.42-3.550.2761410.24012755X-RAY DIFFRACTION100
3.55-3.720.26731420.22822760X-RAY DIFFRACTION99.76
3.72-3.910.19941260.18132765X-RAY DIFFRACTION99.72
3.91-4.160.16731460.15352760X-RAY DIFFRACTION99.55
4.16-4.480.14651400.14032792X-RAY DIFFRACTION99.76
4.48-4.930.15991560.13242785X-RAY DIFFRACTION99.56
4.93-5.640.18721480.15632816X-RAY DIFFRACTION99.5
5.64-7.10.19351490.1832871X-RAY DIFFRACTION99.77
7.1-46.670.20061380.20043066X-RAY DIFFRACTION99.23
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)
12.076784920790.8042183101841.101933718262.037929356760.6004505441013.004380500630.0491960271207-0.00686378622916-0.1114641117540.201430475916-0.07907021502350.07748549323370.446963958579-0.200614719170.01966831665950.846782145432-0.009714964087610.1501032860050.439906171743-0.02843061820770.50824795347830.650623607-0.98141378079837.239089431
22.56769503207-1.02702403264-0.8136926720762.597966805610.3309036169261.561055387150.124216641820.1957671114610.0708596501995-0.00139696025066-0.04685801105860.0351903910732-0.398505112761-0.0248461614617-0.08171975276040.775508205715-0.06513198683050.1494655877820.4973299825420.001260187044430.46435297411834.509844207223.155722260332.0751918054
33.607515055430.2799885310750.8559842391653.967929242222.637758499884.4840754489-0.1116711636040.1160089236760.1339476626810.0923039386076-0.09351510567750.0973817342337-0.1638892622970.07294944291020.1928384958230.99596426852-0.07304319970290.09299383569260.558222630115-0.1099771628490.58596877347223.1478782191-21.76919937628.25417360943
43.39368483745-0.301267191099-1.494459184282.184092227090.0480152436234.52151949434-0.2008641603460.46991285152-0.175703224035-0.140078577436-0.09459677096860.2545176465660.157616481232-1.023282237330.2698799388510.653699469548-0.1068453871560.1635639037251.19426663126-0.07596126953850.62449772683955.847651141620.0966198753.33022990794
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 27 through 215)AA27 - 2151 - 189
22(chain 'B' and resid 27 through 215)BB27 - 2151 - 189
33(chain 'C' and resid 27 through 214)CC27 - 2141 - 188
44(chain 'D' and resid 27 through 215)DD27 - 2151 - 189

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