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- PDB-4tyb: An Ligand-observed Mass Spectrometry-based Approach Integrated in... -

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Basic information

Entry
Database: PDB / ID: 4tyb
TitleAn Ligand-observed Mass Spectrometry-based Approach Integrated into the Fragment Based Lead Discovery Pipeline
ComponentsPolyprotein
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Inhibitor / NS5B / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


serine-type peptidase activity / helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / nucleotide binding / ATP hydrolysis activity / RNA binding / membrane
Similarity search - Function
RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
(2R)-morpholin-4-yl(phenyl)ethanenitrile / RNA-directed RNA polymerase
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / Resolution: 2.93 Å
AuthorsShui, W. / Yang, C. / Lin, J. / Chen, X. / Qin, S. / Chen, S.
CitationJournal: Sci Rep / Year: 2015
Title: A ligand-observed mass spectrometry approach integrated into the fragment based lead discovery pipeline
Authors: Chen, X. / Qin, S. / Chen, S. / Li, J. / Li, L. / Wang, Z. / Wang, Q. / Lin, J. / Yang, C. / Shui, W.
History
DepositionJul 8, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Data collection
Revision 1.2Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyprotein
B: Polyprotein
C: Polyprotein
D: Polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)251,9778
Polymers251,1684
Non-polymers8094
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-2 kcal/mol
Surface area89510 Å2
Unit cell
Length a, b, c (Å)102.450, 102.354, 251.884
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Polyprotein


Mass: 62791.984 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Production host: Escherichia coli (E. coli) / References: UniProt: D0PY27, RNA-directed RNA polymerase
#2: Chemical
ChemComp-3B1 / (2R)-morpholin-4-yl(phenyl)ethanenitrile


Mass: 202.252 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H14N2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: PEG4000, Dithiothreitol, 2-(N-morpholino)ethanesulfonic acid, Glycerin
PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5415 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 23, 2012
RadiationMonochromator: Cu filter / Protocol: LAUE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5415 Å / Relative weight: 1
ReflectionResolution: 2.93→50 Å / Num. obs: 57886 / % possible obs: 99.2 % / Redundancy: 4.9 % / Net I/σ(I): 14.8

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data extraction
HKL-3000data processing
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
REFMAC5.8.0049refinement
REFMAC5.8.0049refinement
RefinementResolution: 2.93→47.41 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.848 / SU B: 18.05 / SU ML: 0.342 / Cross valid method: THROUGHOUT / ESU R Free: 0.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27261 2899 5.1 %RANDOM
Rwork0.20517 ---
obs0.20863 54197 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.21 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0 Å20 Å2
2--0.29 Å2-0 Å2
3----0.47 Å2
Refinement stepCycle: 1 / Resolution: 2.93→47.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16909 0 60 0 16969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01917340
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216505
X-RAY DIFFRACTIONr_angle_refined_deg1.4921.96423524
X-RAY DIFFRACTIONr_angle_other_deg0.817337966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33152163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83222.784704
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.541152912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.03115136
X-RAY DIFFRACTIONr_chiral_restr0.0750.22663
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02119360
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023960
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_it1.3852.7668704
X-RAY DIFFRACTIONr_mcbond_other1.3852.7658699
X-RAY DIFFRACTIONr_mcangle_it2.3614.13910851
X-RAY DIFFRACTIONr_mcangle_other2.3614.1410852
X-RAY DIFFRACTIONr_scbond_it1.3792.9198636
X-RAY DIFFRACTIONr_scbond_other1.3782.9188635
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3524.31912671
X-RAY DIFFRACTIONr_long_range_B_refined3.59421.48119335
X-RAY DIFFRACTIONr_long_range_B_other3.59421.47719332
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.93→3.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 210 -
Rwork0.275 3746 -
obs--94.82 %

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