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- PDB-9mr6: X-ray crystal structure of SAMHD1 from Rhizophagus irregularis -

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Basic information

Entry
Database: PDB / ID: 9mr6
TitleX-ray crystal structure of SAMHD1 from Rhizophagus irregularis
ComponentsHD domain-containing protein
KeywordsANTIVIRAL PROTEIN / dNTPase / hydrolase / metalloenzyme / antiviral / innate immunity
Function / homology
Function and homology information


dGTPase activity / dGTP catabolic process / nucleus
Similarity search - Function
HD-associated domain / HD associated region / : / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / : / PYROPHOSPHATE 2- / HD domain-containing protein
Similarity search - Component
Biological speciesRhizophagus irregularis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsLachowicz, J.C. / Zizola, C. / Grove, T.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM007491 United States
CitationJournal: Jacs Au / Year: 2025
Title: Activation and Allostery in a Fungal SAMHD1 Hydrolase: An Evolutionary Blueprint for dNTP Catabolism.
Authors: Pan, L. / Lachowicz, J.C. / Paddy, I. / Xu, Y. / Yang, Q. / Zizola, C. / Milne, A. / Grove, T.L. / Pandelia, M.E.
History
DepositionJan 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: 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 / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HD domain-containing protein
B: HD domain-containing protein
C: HD domain-containing protein
D: HD domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,77420
Polymers228,5974
Non-polymers3,17716
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20930 Å2
ΔGint-111 kcal/mol
Surface area68810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.359, 85.420, 87.035
Angle α, β, γ (deg.)104.58, 111.65, 99.51
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
HD domain-containing protein


Mass: 57149.258 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizophagus irregularis (fungus) / Gene: RirG_017260 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): T7 Express Competent E. coli / References: UniProt: A0A015K8Z8

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Non-polymers , 5 types, 153 molecules

#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Chemical
ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium tartrate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979354 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979354 Å / Relative weight: 1
ReflectionResolution: 2.27→76.04 Å / Num. obs: 91728 / % possible obs: 94.6 % / Redundancy: 1.8 % / CC1/2: 0.991 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.102 / Rrim(I) all: 0.144 / Χ2: 0.43 / Net I/σ(I): 2.8
Reflection shellResolution: 2.27→2.39 Å / % possible obs: 92.3 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.877 / Num. measured all: 22472 / Num. unique obs: 13106 / CC1/2: 0.48 / Rpim(I) all: 0.875 / Rrim(I) all: 1.239 / Χ2: 0.46 / Net I/σ(I) obs: 0.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→41.5 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.28 4458 4.95 %
Rwork0.2203 --
obs0.2233 90034 93.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14743 0 172 137 15052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01215242
X-RAY DIFFRACTIONf_angle_d0.85620535
X-RAY DIFFRACTIONf_dihedral_angle_d20.1815881
X-RAY DIFFRACTIONf_chiral_restr0.0432181
X-RAY DIFFRACTIONf_plane_restr0.0072585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.30.4121940.36461650X-RAY DIFFRACTION53
2.3-2.320.37221320.37042637X-RAY DIFFRACTION87
2.32-2.350.40681410.34832881X-RAY DIFFRACTION92
2.35-2.380.40181490.34342874X-RAY DIFFRACTION94
2.38-2.410.38081480.32692834X-RAY DIFFRACTION93
2.41-2.450.37211560.30812901X-RAY DIFFRACTION94
2.45-2.480.36321650.30982923X-RAY DIFFRACTION95
2.48-2.520.33821860.29632839X-RAY DIFFRACTION96
2.52-2.560.37271540.29253004X-RAY DIFFRACTION96
2.56-2.60.35341650.28662888X-RAY DIFFRACTION96
2.6-2.640.31261590.27212971X-RAY DIFFRACTION96
2.64-2.690.35191370.26812938X-RAY DIFFRACTION96
2.69-2.740.32451480.26062989X-RAY DIFFRACTION97
2.74-2.80.32051450.26232964X-RAY DIFFRACTION97
2.8-2.860.30361260.2532974X-RAY DIFFRACTION97
2.86-2.930.33361480.25193017X-RAY DIFFRACTION97
2.93-30.31991380.25382951X-RAY DIFFRACTION96
3-3.080.32291550.26572950X-RAY DIFFRACTION97
3.08-3.170.36061560.26372941X-RAY DIFFRACTION96
3.17-3.270.31941280.24982900X-RAY DIFFRACTION95
3.27-3.390.30111670.23162920X-RAY DIFFRACTION95
3.39-3.530.2831680.22052886X-RAY DIFFRACTION94
3.53-3.690.27181610.20992827X-RAY DIFFRACTION93
3.69-3.880.29511640.20222788X-RAY DIFFRACTION92
3.88-4.120.27471150.18832848X-RAY DIFFRACTION92
4.12-4.440.22941500.17212819X-RAY DIFFRACTION92
4.44-4.890.21181340.16412796X-RAY DIFFRACTION92
4.89-5.590.23451630.18362849X-RAY DIFFRACTION93
5.59-7.040.24641570.20072883X-RAY DIFFRACTION94
7.04-41.50.18571490.15722934X-RAY DIFFRACTION96

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