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- PDB-7t7h: Crystal structure of Vaccinia Virus decapping enzyme D9 in comple... -

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Basic information

Entry
Database: PDB / ID: 7t7h
TitleCrystal structure of Vaccinia Virus decapping enzyme D9 in complex with inhibitor CP100356
ComponentsDNA repair NTP-phosphohydrolase
KeywordsVIRAL PROTEIN/VIRAL PROTEIN INHIBITOR / decapping enzyme / nudix / inhibitor / VIRAL PROTEIN-VIRAL PROTEIN INHIBITOR complex
Function / homologyViral protein D9 / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / hydrolase activity / Chem-G7R / NTP-phosphohydrolase
Function and homology information
Biological speciesVaccinia virus Western Reserve
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78000262178 Å
AuthorsPeters, J.K. / Gross, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5F32GM133084 United States
CitationJournal: Acs Chem.Biol. / Year: 2022
Title: Fluorescence-Based Activity Screening Assay Reveals Small Molecule Inhibitors of Vaccinia Virus mRNA Decapping Enzyme D9.
Authors: Bednarczyk, M. / Peters, J.K. / Kasprzyk, R. / Starek, J. / Warminski, M. / Spiewla, T. / Mugridge, J.S. / Gross, J.D. / Jemielity, J. / Kowalska, J.
History
DepositionDec 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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: DNA repair NTP-phosphohydrolase
B: DNA repair NTP-phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3716
Polymers52,2042
Non-polymers1,1674
Water3,495194
1
A: DNA repair NTP-phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7094
Polymers26,1021
Non-polymers6073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA repair NTP-phosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6632
Polymers26,1021
Non-polymers5611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.77, 82.77, 96.31
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILESERSERchain 'A'AA3 - 613 - 61
12VALVALLEULEUchain 'A'AA71 - 9171 - 91
13ASPASPSERSERchain 'A'AA100 - 212100 - 212
21ILEILESERSERchain 'B'BB3 - 613 - 61
22VALVALLEULEUchain 'B'BB71 - 9171 - 91
23ASPASPSERSERchain 'B'BB100 - 212100 - 212

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Components

#1: Protein DNA repair NTP-phosphohydrolase / MutT motif/mRNA decapping enzyme / NTP-phosphohydrolase / Putative D9R


Mass: 26102.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus Western Reserve
Gene: D9R, VACV_BRZ_SERRO2_112, VACV_CTGV_ALEH2_114, VACV_CTGV_CG04_114, VACV_CTGV_MI233-114, VACV_CTGV_VI04_114, VAC_IHDW1_116, VAC_TKT3_104, VAC_TKT4_104, VAC_TP3_119, VAC_TP5_119, VACV_CTGV_CM01_ ...Gene: D9R, VACV_BRZ_SERRO2_112, VACV_CTGV_ALEH2_114, VACV_CTGV_CG04_114, VACV_CTGV_MI233-114, VACV_CTGV_VI04_114, VAC_IHDW1_116, VAC_TKT3_104, VAC_TKT4_104, VAC_TP3_119, VAC_TP5_119, VACV_CTGV_CM01_114, VACV_TT10_141, VACV_TT11_141, VACV_TT12_141, VACV_TT8_141, VACV_TT9_141
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L7QJE0
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-G7R / 4-(6,7-dimethoxy-3,4-dihydroisoquinolin-2(1H)-yl)-N-[2-(3,4-dimethoxyphenyl)ethyl]-6,7-dimethoxyquinazolin-2-amine


Mass: 560.641 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C31H36N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
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: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 100mM NaF

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.78→62.7732227509 Å / Num. obs: 44130 / % possible obs: 99.79 % / Redundancy: 12.9 % / Biso Wilson estimate: 33.2653021128 Å2 / Rmerge(I) obs: 0.04373 / Rrim(I) all: 0.04555 / Net I/σ(I): 30.35
Reflection shellResolution: 1.78→1.844 Å / Rmerge(I) obs: 0.9509 / Num. unique obs: 4244

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SEV

7sev


Resolution: 1.78000262178→62.7732227509 Å / SU ML: 0.176396858988 / Cross valid method: FREE R-VALUE / σ(F): 1.35113385529 / Phase error: 21.7555778038
RfactorNum. reflection% reflection
Rfree0.219365876242 2000 4.53237247037 %
Rwork0.187110154184 42127 -
obs0.188553271362 44127 99.7829183909 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.0041316931 Å2
Refinement stepCycle: LAST / Resolution: 1.78000262178→62.7732227509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 84 194 3572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01926224958273434
X-RAY DIFFRACTIONf_angle_d1.985279124064612
X-RAY DIFFRACTIONf_chiral_restr0.10225286971509
X-RAY DIFFRACTIONf_plane_restr0.0102652015798571
X-RAY DIFFRACTIONf_dihedral_angle_d17.04788615661353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78000262178-1.82450.2652821638491380.2448615300292895X-RAY DIFFRACTION97.1492632928
1.8245-1.87390.2899608101911390.2273681141892939X-RAY DIFFRACTION100
1.8739-1.9290.2591350467341420.2165860089282989X-RAY DIFFRACTION100
1.929-1.99130.2730229717381400.2016594411942958X-RAY DIFFRACTION100
1.9913-2.06240.2150672200571420.190576483342990X-RAY DIFFRACTION100
2.0624-2.1450.2519035875171420.1913416712862977X-RAY DIFFRACTION100
2.145-2.24260.2205461990591430.1915263769553014X-RAY DIFFRACTION100
2.2426-2.36090.2269100910891420.19319055462994X-RAY DIFFRACTION100
2.3609-2.50880.2465240206031420.1974992042362993X-RAY DIFFRACTION99.9681122449
2.5088-2.70250.2465721224291430.2024591152053023X-RAY DIFFRACTION100
2.7025-2.97450.23010748631430.198577677723016X-RAY DIFFRACTION100
2.9745-3.40490.2142605324021450.191838937143035X-RAY DIFFRACTION100
3.4049-4.28960.2005154581021450.167069913453080X-RAY DIFFRACTION100
4.2896-62.77322275090.199226018511540.1782731899723224X-RAY DIFFRACTION99.8817267889
Refinement TLS params.Method: refined / Origin x: -23.5363735217 Å / Origin y: 11.1709680487 Å / Origin z: -14.3823393687 Å
111213212223313233
T0.250673955831 Å2-0.0126745939079 Å20.00735762608956 Å2-0.196195607548 Å2-0.0169414073262 Å2--0.300445239258 Å2
L0.924721969837 °2-0.254514203356 °20.908672428107 °2-0.836578668185 °2-0.20858907312 °2--2.21605906551 °2
S0.0853751746137 Å °0.0156761532887 Å °-0.083126587555 Å °-0.170742027798 Å °-0.00867969368539 Å °0.0769849176189 Å °0.185079135598 Å °-0.0979711622268 Å °-0.0904013901135 Å °
Refinement TLS groupSelection details: all

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