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- PDB-9dfw: X-ray crystal structure of an engineered Viperin-like enzyme from... -

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Basic information

Entry
Database: PDB / ID: 9dfw
TitleX-ray crystal structure of an engineered Viperin-like enzyme from T. virens with bound CTP and SAM
ComponentsRadical SAM core domain-containing protein
KeywordsANTIVIRAL PROTEIN / engineered viperin-like enzyme / viperin-like enzyme / CTP / SAM / 4Fe-4S cluster / ddhCTP
Function / homology
Function and homology information


catalytic activity / 4 iron, 4 sulfur cluster binding / defense response to virus / mitochondrion / metal ion binding
Similarity search - Function
: / 4Fe-4S single cluster domain / Elp3/MiaB/NifB / Elongator protein 3, MiaB family, Radical SAM / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / Radical SAM core domain-containing protein
Similarity search - Component
Biological speciesTrichoderma virens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.677 Å
AuthorsLachowicz, J.C. / Bonanno, J.B. / Grove, T.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM007491 United States
CitationJournal: Structure / Year: 2025
Title: Structural insights from active site variants and beta-8 loop interactions in viperin-like enzymes.
Authors: Lachowicz, J.C. / Grudman, S. / Bonanno, J.B. / Fiser, A. / Grove, T.L.
History
DepositionAug 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Radical SAM core domain-containing protein
B: Radical SAM core domain-containing protein
C: Radical SAM core domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,44918
Polymers109,1073
Non-polymers4,34115
Water12,791710
1
A: Radical SAM core domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1288
Polymers36,3691
Non-polymers1,7587
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Radical SAM core domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6024
Polymers36,3691
Non-polymers1,2333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Radical SAM core domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7196
Polymers36,3691
Non-polymers1,3505
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.131, 85.131, 110.471
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Radical SAM core domain-containing protein


Mass: 36369.113 Da / Num. of mol.: 3
Mutation: residues 256-261 (Uniprot numbering) DRNGQQ mutated to NCTGGRKD, residues 197-198 (Uniprot numbering) mutated from VT to IE (residue numbers 198-199 in the model)
Source method: isolated from a genetically manipulated source
Details: residues have been swapped with mus musculus viperin (Uniprot: Q8CBB9)
Source: (gene. exp.) Trichoderma virens (fungus) / Strain: Gv29-8 / Gene: TRIVIDRAFT_58105 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G9MQB8

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Non-polymers , 7 types, 725 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / 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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES (pH 7.0), 10% (w/v) PEG 6K

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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: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.677→61.323 Å / Num. obs: 102720 / % possible obs: 100 % / Redundancy: 9.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.076 / Rrim(I) all: 0.17 / Net I/σ(I): 9
Reflection shellResolution: 1.677→1.705 Å / Rmerge(I) obs: 2.332 / Mean I/σ(I) obs: 1 / Num. unique obs: 5167 / CC1/2: 0.358 / Rpim(I) all: 1.167 / Rrim(I) all: 2.612

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.677→19.86 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.532 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18793 4939 4.8 %RANDOM
Rwork0.1552 ---
obs0.15675 97622 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20.18 Å20 Å2
2--0.37 Å2-0 Å2
3----1.19 Å2
Refinement stepCycle: 1 / Resolution: 1.677→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6920 0 231 710 7861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0137427
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176645
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.64210057
X-RAY DIFFRACTIONr_angle_other_deg1.4111.58315513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.065882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29623.317401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.437151311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7681539
X-RAY DIFFRACTIONr_chiral_restr0.1190.2948
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028184
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021543
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1852.6193504
X-RAY DIFFRACTIONr_mcbond_other2.1852.6193504
X-RAY DIFFRACTIONr_mcangle_it3.0633.924388
X-RAY DIFFRACTIONr_mcangle_other3.0633.924389
X-RAY DIFFRACTIONr_scbond_it3.4692.9753923
X-RAY DIFFRACTIONr_scbond_other3.4612.9733921
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2724.3095632
X-RAY DIFFRACTIONr_long_range_B_refined6.42431.5288335
X-RAY DIFFRACTIONr_long_range_B_other6.3430.9818160
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.677→1.72 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 333 -
Rwork0.31 7182 -
obs--99.64 %

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