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- PDB-8rsn: macrodomain-fused SirTM (Mfs1) from Fusarium oxysporum f. sp. cub... -

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Basic information

Entry
Database: PDB / ID: 8rsn
Titlemacrodomain-fused SirTM (Mfs1) from Fusarium oxysporum f. sp. cubense race 1
ComponentsADP-ribose 1''-phosphate phosphatase
KeywordsHYDROLASE / ADP-RIBOSYLATION / ADP-RIBOSE / ADP-RIBOSYLHYDROLASE / Lipoylation / Metalloenzyme
Function / homology
Function and homology information


ADP-ribose 1''-phosphate phosphatase / phosphoprotein phosphatase activity / metal ion binding
Similarity search - Function
Sirtuin, catalytic core small domain superfamily / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like
Similarity search - Domain/homology
: / THIOCYANATE ION / ADP-ribose 1''-phosphate phosphatase
Similarity search - Component
Biological speciesFusarium oxysporum f. sp. cubense race 1 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.219 Å
AuthorsAriza, A.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Wellcome Trust210634 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R007195/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W016613/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/X007472/1 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Evolutionary and molecular basis of ADP-ribosylation reversal by zinc-dependent macrodomains.
Authors: Ariza, A. / Liu, Q. / Cowieson, N.P. / Ahel, I. / Filippov, D.V. / Rack, J.G.M.
History
DepositionJan 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 16, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation_author.name / _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: ADP-ribose 1''-phosphate phosphatase
B: ADP-ribose 1''-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,66523
Polymers132,4372
Non-polymers1,22821
Water4,540252
1
A: ADP-ribose 1''-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,86512
Polymers66,2181
Non-polymers64711
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribose 1''-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,79911
Polymers66,2181
Non-polymers58110
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.739, 135.089, 147.625
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLU / End label comp-ID: GLU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 8 - 597 / Label seq-ID: 10 - 599

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ADP-ribose 1''-phosphate phosphatase / Macrodomain-fused SirTM (Mfs1) from Fusarium oxysporum f. sp. cubense race 1


Mass: 66218.297 Da / Num. of mol.: 2 / Mutation: N419A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium oxysporum f. sp. cubense race 1 (fungus)
Strain: IMI 141109 / Gene: Focb16_v015632 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A559KX76, ADP-ribose 1''-phosphate phosphatase

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Non-polymers , 5 types, 273 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 200 mM KSC 100 mM BisTris-propane pH 7.5 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.28229 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28229 Å / Relative weight: 1
ReflectionResolution: 2.219→147.6 Å / Num. obs: 61954 / % possible obs: 100 % / Redundancy: 11.9 % / CC1/2: 0.999 / Net I/σ(I): 13.2
Reflection shellResolution: 2.22→2.28 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4501 / CC1/2: 0.512 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.219→99.859 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 15.6 / SU ML: 0.183 / Cross valid method: FREE R-VALUE / ESU R: 0.275 / ESU R Free: 0.22
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2532 3030 4.902 %
Rwork0.2031 58779 -
all0.206 --
obs-61809 99.787 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 55.321 Å2
Baniso -1Baniso -2Baniso -3
1--0.413 Å20 Å2-0 Å2
2--0.8 Å20 Å2
3----0.387 Å2
Refinement stepCycle: LAST / Resolution: 2.219→99.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8313 0 63 252 8628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0128590
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168153
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.65211633
X-RAY DIFFRACTIONr_angle_other_deg0.5541.57618787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.94151064
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.004559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.779101434
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg19.969108
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.93510366
X-RAY DIFFRACTIONr_chiral_restr0.0760.21324
X-RAY DIFFRACTIONr_chiral_restr_other0.0230.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210078
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021906
X-RAY DIFFRACTIONr_nbd_refined0.2170.21702
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.27250
X-RAY DIFFRACTIONr_nbtor_refined0.1810.24176
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.24718
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0130.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1740.213
X-RAY DIFFRACTIONr_nbd_other0.2310.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1890.27
X-RAY DIFFRACTIONr_mcbond_it5.0294.1364289
X-RAY DIFFRACTIONr_mcbond_other4.9884.1364284
X-RAY DIFFRACTIONr_mcangle_it7.4087.3895330
X-RAY DIFFRACTIONr_mcangle_other7.4087.395331
X-RAY DIFFRACTIONr_scbond_it5.6564.6494301
X-RAY DIFFRACTIONr_scbond_other5.6564.6474299
X-RAY DIFFRACTIONr_scangle_it8.2198.2956301
X-RAY DIFFRACTIONr_scangle_other8.2178.2956301
X-RAY DIFFRACTIONr_lrange_it10.82939.0699273
X-RAY DIFFRACTIONr_lrange_other10.82638.8239231
X-RAY DIFFRACTIONr_ncsr_local_group_10.0950.0516296
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.094870.05008
12AX-RAY DIFFRACTIONLocal ncs0.094870.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.219-2.2770.3521960.35542390.35545110.9070.998.31520.357
2.277-2.3390.3492190.32341510.32443840.910.92299.68070.318
2.339-2.4070.2931950.28641080.28643050.9390.94499.95350.275
2.407-2.4810.3021860.24939720.25141650.9440.96199.83190.234
2.481-2.5620.2972050.23838320.24140460.9430.96699.77760.221
2.562-2.6520.2812000.22737090.2339150.9480.96999.84670.207
2.652-2.7520.2751820.21535890.21837730.9550.97299.9470.192
2.752-2.8640.2941850.20834620.21336480.9420.97299.97260.183
2.864-2.9920.2641730.18833180.19234920.9570.97899.97140.167
2.992-3.1370.2371620.18332090.18633710.9670.981000.165
3.137-3.3070.2531720.18830110.19131850.960.9899.93720.174
3.307-3.5070.2321460.19528870.19730340.9660.98199.9670.185
3.507-3.7490.2271460.19427050.19628510.9680.9821000.186
3.749-4.0490.2161430.1825150.18226580.9730.981000.172
4.049-4.4350.2261190.15823670.16124870.970.98599.95980.155
4.435-4.9570.1961040.1621390.16122440.9760.98599.95540.158
4.957-5.7210.2851060.19918990.20420050.9610.981000.195
5.721-7.0020.238820.19316210.19617050.9770.98199.88270.19
7.002-9.8780.21680.16812840.1713530.9760.98499.92610.172
9.878-99.8590.309410.2517620.2548090.9240.9499.25830.262
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)
10.63290.14380.04560.52820.26270.818-0.0356-0.0294-0.00210.01830.0933-0.0113-0.06130.0102-0.05770.01880.00320.00630.0957-0.01110.00621.4156-5.055-35.3993
20.6373-0.025-0.24641.3227-0.08230.5885-0.0531-0.0266-0.18350.2601-0.02240.08040.12340.10680.07550.09030.01490.03020.05650.01730.059420.2326-28.5629-38.443
Refinement TLS groupSelection: ALL

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