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- PDB-9dfn: X-ray crystal structure of the second viperin-like enzyme from Tr... -

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Basic information

Entry
Database: PDB / ID: 9dfn
TitleX-ray crystal structure of the second viperin-like enzyme from Trichoderma virens with bound CTP and SAM
ComponentsRadical SAM core domain-containing protein
KeywordsANTIVIRAL PROTEIN / viperin / 4fe-4s cluster / radical SAM / 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: 1.5 Å
AuthorsLachowicz, J.C. / Grove, T.G. / Bonanno, J.B.
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 19, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6475
Polymers37,3791
Non-polymers1,2694
Water6,485360
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.808, 57.838, 157.692
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Radical SAM core domain-containing protein


Mass: 37378.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoderma virens (fungus) / Strain: Gv29-8 / Gene: TRIVIDRAFT_46896 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G9N0G3

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Non-polymers , 5 types, 364 molecules

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


Mass: 351.640 Da / Num. of mol.: 1 / 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.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Bis-Tris (pH 6.5), 20% (w/v) PGG MME 5K

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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: 0.920105 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 1.5→32.576 Å / Num. obs: 54980 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.072 / Rrim(I) all: 0.185 / Net I/σ(I): 6.2
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 1.246 / Num. unique obs: 5427 / CC1/2: 0.746 / Rpim(I) all: 0.509 / Rrim(I) all: 1.347 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→19.71 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.004 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19674 2000 3.6 %RANDOM
Rwork0.16936 ---
obs0.17034 52954 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.973 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å20 Å2-0 Å2
2--2.99 Å20 Å2
3----1.69 Å2
Refinement stepCycle: 1 / Resolution: 1.5→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2311 0 65 360 2736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122468
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162310
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.6563340
X-RAY DIFFRACTIONr_angle_other_deg0.5581.5895323
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6325294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.256519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16410456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1040.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022880
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02598
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_it1.411.6521146
X-RAY DIFFRACTIONr_mcbond_other1.411.6521146
X-RAY DIFFRACTIONr_mcangle_it1.9772.9611432
X-RAY DIFFRACTIONr_mcangle_other1.9772.961433
X-RAY DIFFRACTIONr_scbond_it2.7721.921322
X-RAY DIFFRACTIONr_scbond_other2.7751.9231311
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.273.3771891
X-RAY DIFFRACTIONr_long_range_B_refined5.75819.272985
X-RAY DIFFRACTIONr_long_range_B_other5.43417.142843
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 146 -
Rwork0.304 3872 -
obs--99.98 %

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