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- PDB-4ty9: An Ligand-observed Mass Spectrometry-based Approach Integrated in... -

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Basic information

Entry
Database: PDB / ID: 4ty9
TitleAn Ligand-observed Mass Spectrometry-based Approach Integrated into the Fragment Based Lead Discovery Pipeline
ComponentsPolyprotein
KeywordsTRANAFERASE/TRANSFERASE INHIBITOR / NS5B / TRANAFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


serine-type peptidase activity / helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / 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
5-(trifluoromethyl)pyridin-2-amine / RNA-directed RNA polymerase
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / Resolution: 2.78 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 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Derived calculations
Revision 1.2Sep 2, 2015Group: Data collection
Revision 1.3Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)251,2305
Polymers251,0684
Non-polymers1621
Water00
1
A: Polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9292
Polymers62,7671
Non-polymers1621
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyprotein


Theoretical massNumber of molelcules
Total (without water)62,7671
Polymers62,7671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Polyprotein


Theoretical massNumber of molelcules
Total (without water)62,7671
Polymers62,7671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Polyprotein


Theoretical massNumber of molelcules
Total (without water)62,7671
Polymers62,7671
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.774, 101.643, 251.582
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: 62766.992 Da / Num. of mol.: 4 / Mutation: I539L, G549S, W550M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Production host: Escherichia coli (E. coli) / References: UniProt: D0PY27
#2: Chemical ChemComp-3B0 / 5-(trifluoromethyl)pyridin-2-amine


Mass: 162.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H5F3N2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.22 %
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 25, 2013
RadiationMonochromator: Cu filter / Protocol: LAUE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5415 Å / Relative weight: 1
ReflectionResolution: 2.78→50 Å / Num. obs: 66538 / % possible obs: 99.9 % / Redundancy: 6.5 % / Net I/σ(I): 12.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data collection
HKL-3000data extraction
HKL-3000data processing
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 2.78→42.79 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.876 / SU B: 15.728 / SU ML: 0.309 / Cross valid method: THROUGHOUT / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27349 3368 5.1 %RANDOM
Rwork0.20776 ---
obs0.2111 62833 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å2-0 Å20 Å2
2--0.12 Å2-0 Å2
3----0.36 Å2
Refinement stepCycle: final / Resolution: 2.78→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16872 0 11 0 16883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01917239
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216433
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.96323384
X-RAY DIFFRACTIONr_angle_other_deg0.834337797
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42752160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89822.8700
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.315152924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.26715136
X-RAY DIFFRACTIONr_chiral_restr0.0790.22660
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02119278
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023921
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_it1.8613.3818689
X-RAY DIFFRACTIONr_mcbond_other1.863.388687
X-RAY DIFFRACTIONr_mcangle_it3.0495.06210832
X-RAY DIFFRACTIONr_mcangle_other3.0495.06210833
X-RAY DIFFRACTIONr_scbond_it1.9183.5658550
X-RAY DIFFRACTIONr_scbond_other1.9173.5658549
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1695.26712552
X-RAY DIFFRACTIONr_long_range_B_refined4.64826.319373
X-RAY DIFFRACTIONr_long_range_B_other4.64826.30319374
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.779→2.851 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 232 -
Rwork0.277 4501 -
obs--98.26 %

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