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- PDB-7xry: Crystal structure of MERS main protease in complex with inhibitor... -

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Basic information

Entry
Database: PDB / ID: 7xry
TitleCrystal structure of MERS main protease in complex with inhibitor YH-53
ComponentsORF1a
KeywordsVIRAL PROTEIN/INHIBITOR / VIRAL PROTEIN-INHIBITOR COMPLEX
Function / homologymain 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 / Chem-HUR
Function and homology information
Biological speciesMiddle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsLin, C. / Zhong, F.L. / Zhou, X.L. / Li, J. / Zhang, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Viruses / Year: 2022
Title: Structural Basis for the Inhibition of Coronaviral Main Proteases by a Benzothiazole-Based Inhibitor.
Authors: Hu, X. / Lin, C. / Xu, Q. / Zhou, X. / Zeng, P. / McCormick, P.J. / Jiang, H. / Li, J. / Zhang, J.
History
DepositionMay 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ORF1a
B: ORF1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8304
Polymers65,6792
Non-polymers1,1512
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-13 kcal/mol
Surface area24370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.016, 93.800, 102.156
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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

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Components

#1: Protein ORF1a


Mass: 32839.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus
Gene: orf1ab / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
#2: Chemical ChemComp-HUR / N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide


Mass: 575.679 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H33N5O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M Sodium formate, 0.1M BICINE pH8.5 20% PEG5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.99→44.86 Å / Num. obs: 53633 / % possible obs: 99.9 % / Redundancy: 9.7 % / Biso Wilson estimate: 27.3489656876 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 11
Reflection shellResolution: 1.99→2.09 Å / Rmerge(I) obs: 0.926 / Num. unique obs: 53633

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VTC

7vtc


Resolution: 1.99→44.86 Å / SU ML: 0.273274265818 / Cross valid method: FREE R-VALUE / σ(F): 1.34360112772 / Phase error: 24.1207739763
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.253470791395 2736 5.10972079559 %
Rwork0.223588675513 50809 -
obs0.225103354667 53545 99.8098682126 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.9946313228 Å2
Refinement stepCycle: LAST / Resolution: 1.99→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4488 0 82 203 4773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007355973011514687
X-RAY DIFFRACTIONf_angle_d0.9211157672396402
X-RAY DIFFRACTIONf_chiral_restr0.0628141132462736
X-RAY DIFFRACTIONf_plane_restr0.00634052510193810
X-RAY DIFFRACTIONf_dihedral_angle_d3.746697857052674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.02150.3388456914541310.2718355707382487X-RAY DIFFRACTION98.0524344569
2.0215-2.05820.3990402468521360.2601423881822512X-RAY DIFFRACTION99.8491704374
2.0582-2.09780.3261205069681310.2567709407822490X-RAY DIFFRACTION99.9618611747
2.0978-2.14060.2811369043451410.2494901731732494X-RAY DIFFRACTION99.9620637329
2.1406-2.18720.275555023331330.2326015520292523X-RAY DIFFRACTION99.9247554552
2.1872-2.23810.276151936831550.2341097433872509X-RAY DIFFRACTION99.9624765478
2.2381-2.2940.2903175909511390.2380531742742499X-RAY DIFFRACTION99.9621068587
2.294-2.3560.2604878378971310.2264236047282533X-RAY DIFFRACTION99.9624765478
2.356-2.42540.2822962717871270.2313828506542531X-RAY DIFFRACTION100
2.4254-2.50360.2655376879311330.2295111705132514X-RAY DIFFRACTION99.8867924528
2.5036-2.59310.2591778468511540.2238949900392507X-RAY DIFFRACTION99.96243426
2.5931-2.69690.2701885259391470.2299738195182522X-RAY DIFFRACTION99.8877245509
2.6969-2.81970.2480871689171320.2257354550732530X-RAY DIFFRACTION99.9249249249
2.8197-2.96830.2888485297731430.232623348282538X-RAY DIFFRACTION100
2.9683-3.15420.2587855317271380.2333285572162550X-RAY DIFFRACTION99.9628114541
3.1542-3.39770.2606457084831140.225032077652582X-RAY DIFFRACTION99.9629217649
3.3977-3.73940.2319532976911270.2227311976022576X-RAY DIFFRACTION99.9260628466
3.7394-4.28020.2013225110491230.1986000607922589X-RAY DIFFRACTION99.9631404349
4.2802-5.39110.2273552489371410.1995978720782619X-RAY DIFFRACTION99.9637812387
5.3911-44.860.2300403390651600.2223339306062704X-RAY DIFFRACTION99.2720970537

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