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- PDB-7qt9: Room temperature In-situ SARS-CoV-2 MPRO with bound Z4439011584 -

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Basic information

Entry
Database: PDB / ID: 7qt9
TitleRoom temperature In-situ SARS-CoV-2 MPRO with bound Z4439011584
ComponentsNon-structural protein 6
KeywordsVIRAL PROTEIN / Protease / Main protease / SARS-CoV-2
Function / homology
Function and homology information


main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Trypsin-like serine proteases / Thrombin, subunit H / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSevere acute respiratory syndrome coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsHorrell, S. / Gildae, R.J. / Axford, D. / Owen, C.D. / Lukacik, P. / Strain-Damerell, C. / Owen, R.L. / Walsh, M.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Science and Technology Funding Council United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: xia2.multiplex: a multi-crystal data-analysis pipeline.
Authors: Gildea, R.J. / Beilsten-Edmands, J. / Axford, D. / Horrell, S. / Aller, P. / Sandy, J. / Sanchez-Weatherby, J. / Owen, C.D. / Lukacik, P. / Strain-Damerell, C. / Owen, R.L. / Walsh, M.A. / Winter, G.
History
DepositionJan 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2233
Polymers33,6971
Non-polymers5262
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint2 kcal/mol
Surface area14290 Å2
Unit cell
Length a, b, c (Å)45.199, 54.485, 115.725
Angle α, β, γ (deg.)90.000, 101.092, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Non-structural protein 6 / Non-structural protein 8 / Papain-like proteinase


Mass: 33697.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus
Gene: ORF1ab / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A7M2P846
#2: Chemical ChemComp-UJ1 / N-(5-tert-butyl-1H-pyrazol-3-yl)-N-[(1R)-2-[(2-ethyl-6-methylphenyl)amino]-2-oxo-1-(pyridin-3-yl)ethyl]propanamide


Mass: 447.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H33N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5 / Details: 11% (v/v) PEG 4K, 5% (v/v) DMSO, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.43→56.846 Å / Num. obs: 10345 / % possible obs: 97.9 % / Redundancy: 5.9 % / CC1/2: 0.987 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.073 / Rsym value: 0.183 / Net I/σ(I): 10.8
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.241 / Num. unique obs: 1038 / CC1/2: 0.305 / Rpim(I) all: 0.578 / Rrim(I) all: 1.38 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AEH

7aeh


Resolution: 2.43→56.846 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.953 / SU B: 21.705 / SU ML: 0.207 / Cross valid method: FREE R-VALUE / ESU R: 1.571 / ESU R Free: 0.248
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2003 543 5.252 %
Rwork0.1496 9796 -
all0.152 --
obs-10339 97.87 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 45.722 Å2
Baniso -1Baniso -2Baniso -3
1--0.609 Å2-0 Å20.211 Å2
2---0.549 Å2-0 Å2
3---0.998 Å2
Refinement stepCycle: LAST / Resolution: 2.43→56.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 37 23 2407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132447
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152271
X-RAY DIFFRACTIONr_angle_refined_deg1.9031.643328
X-RAY DIFFRACTIONr_angle_other_deg1.3591.5765206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1615305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3523.033122
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg8.494101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.81815386
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg0.055151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3551511
X-RAY DIFFRACTIONr_chiral_restr0.0760.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022832
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02586
X-RAY DIFFRACTIONr_nbd_refined0.2110.2437
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.22142
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21203
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21223
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.250
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2270.218
X-RAY DIFFRACTIONr_nbd_other0.270.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1170.27
X-RAY DIFFRACTIONr_mcbond_it1.8313.3631220
X-RAY DIFFRACTIONr_mcbond_other1.8263.3621219
X-RAY DIFFRACTIONr_mcangle_it2.9125.0471525
X-RAY DIFFRACTIONr_mcangle_other2.9135.0491526
X-RAY DIFFRACTIONr_scbond_it2.4833.731227
X-RAY DIFFRACTIONr_scbond_other2.4823.7321228
X-RAY DIFFRACTIONr_scangle_it4.015.4671803
X-RAY DIFFRACTIONr_scangle_other4.0095.4681804
X-RAY DIFFRACTIONr_lrange_it5.56339.3712584
X-RAY DIFFRACTIONr_lrange_other5.56239.362584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.4930.381420.268724X-RAY DIFFRACTION97.3316
2.493-2.5620.306310.273721X-RAY DIFFRACTION98.0443
2.562-2.6360.277480.251660X-RAY DIFFRACTION97.5207
2.636-2.7170.298420.237631X-RAY DIFFRACTION96.1429
2.717-2.8060.299320.237647X-RAY DIFFRACTION98.4058
2.806-2.9040.252380.226625X-RAY DIFFRACTION98.6607
2.904-3.0140.276410.196615X-RAY DIFFRACTION99.3939
3.014-3.1370.251320.175556X-RAY DIFFRACTION97.8369
3.137-3.2760.204360.154557X-RAY DIFFRACTION99.1639
3.276-3.4360.119230.148540X-RAY DIFFRACTION98.0836
3.436-3.6220.231250.135511X-RAY DIFFRACTION98.1685
3.622-3.8410.17260.126484X-RAY DIFFRACTION98.646
3.841-4.1060.156260.104457X-RAY DIFFRACTION98.9754
4.106-4.4350.115290.1422X-RAY DIFFRACTION98.0435
4.435-4.8570.157140.095387X-RAY DIFFRACTION97.8049
4.857-5.4290.136150.107362X-RAY DIFFRACTION97.9221
5.429-6.2670.174160.126306X-RAY DIFFRACTION96.1194
6.267-7.6690.133130.131267X-RAY DIFFRACTION97.2222
7.669-10.8210.10790.098205X-RAY DIFFRACTION94.6903
10.821-56.8460.3450.14119X-RAY DIFFRACTION92.5373
Refinement TLS params.Method: refined / Origin x: -2.1659 Å / Origin y: 0.7661 Å / Origin z: 13.0578 Å
111213212223313233
T0.0136 Å20.0164 Å2-0.0104 Å2-0.027 Å2-0.0139 Å2--0.0103 Å2
L2.381 °21.3085 °2-0.4748 °2-2.2119 °2-0.3 °2--1.4999 °2
S0.0048 Å °-0.1186 Å °-0.0003 Å °0.0081 Å °-0.0437 Å °-0.0066 Å °0.0197 Å °0.0182 Å °0.0389 Å °
Refinement TLS groupSelection: ALL

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