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- PDB-7n7i: X-ray crystal structure of Viperin-like enzyme from Trichoderma virens -

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Basic information

Entry
Database: PDB / ID: 7n7i
TitleX-ray crystal structure of Viperin-like enzyme from Trichoderma virens
ComponentsViperin-like enzyme
KeywordsANTIVIRAL PROTEIN / radical SAM protein / metalloprotein / antiviral / ddh-synthase
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
S-ADENOSYLMETHIONINE / IRON/SULFUR CLUSTER / URIDINE 5'-TRIPHOSPHATE / Radical SAM core domain-containing protein
Similarity search - Component
Biological speciesHypocrea virens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsGrove, T.L. / Almo, S.C. / Bonanno, J.B. / Lachowicz, J.C. / Gizzi, A.G.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21-AI133329 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01-GM118303-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54-GM093342 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54-GM094662 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM007491
CitationJournal: Biochemistry / Year: 2021
Title: Structural Insight into the Substrate Scope of Viperin and Viperin-like Enzymes from Three Domains of Life.
Authors: Lachowicz, J.C. / Gizzi, A.S. / Almo, S.C. / Grove, T.L.
History
DepositionJun 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _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
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Viperin-like enzyme
B: Viperin-like enzyme
C: Viperin-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,09512
Polymers113,3933
Non-polymers3,7039
Water00
1
A: Viperin-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0324
Polymers37,7981
Non-polymers1,2343
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Viperin-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0324
Polymers37,7981
Non-polymers1,2343
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Viperin-like enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0324
Polymers37,7981
Non-polymers1,2343
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.943, 85.943, 111.718
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 18 - 298 / Label seq-ID: 40 - 320

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC

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Components

#1: Protein Viperin-like enzyme / Elp3 domain-containing protein


Mass: 37797.598 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypocrea virens (strain Gv29-8 / FGSC 10586) (fungus)
Strain: Gv29-8 / FGSC 10586 / Gene: TRIVIDRAFT_58105 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G9MQB8
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: UTP*YM
Has ligand of interestY

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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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl, pH 8.5, 0.2 M sodium chloride, 25% (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: 0.9893 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9893 Å / Relative weight: 1
ReflectionResolution: 3.19→28.14 Å / Num. obs: 15361 / % possible obs: 98.8 % / Redundancy: 10.3 % / CC1/2: 0.982 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.129 / Rrim(I) all: 0.409 / Net I/σ(I): 8.46
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.19-3.419.71.425980.6160.4731.1893.9
9.02-28.1410.90.0956760.9970.030.197.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VSL

5vsl


Resolution: 3.19→28.14 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 0.11 / Phase error: 26.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2601 1474 4.87 %
Rwork0.2264 28799 -
obs0.228 15195 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.75 Å2 / Biso mean: 42.9874 Å2 / Biso min: 13.3 Å2
Refinement stepCycle: final / Resolution: 3.19→28.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6741 0 192 0 6933
Biso mean--46.76 --
Num. residues----837
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2529X-RAY DIFFRACTION0.928TORSIONAL
12B2529X-RAY DIFFRACTION0.928TORSIONAL
13C2529X-RAY DIFFRACTION0.928TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.19-3.290.38941380.33062295243386
3.29-3.410.35741760.320125462722100
3.41-3.550.32761440.294926582802100
3.55-3.710.30121400.27926922832100
3.71-3.90.31181320.257826712803100
3.9-4.140.23441080.223226572765100
4.15-4.470.21421480.196925942742100
4.47-4.910.2186880.187126982786100
4.91-5.620.27221360.194926732809100
5.62-7.050.19861440.201826642808100
7.06-28.140.16311200.163226512771100

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