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- PDB-4wxr: X-ray crystal structure of NS3 Helicase from HCV with a bound inh... -

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Basic information

Entry
Database: PDB / ID: 4wxr
TitleX-ray crystal structure of NS3 Helicase from HCV with a bound inhibitor at 2.42 A resolution
ComponentsNS3
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Helicase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


: / symbiont-mediated transformation of host cell / serine-type peptidase activity / ribonucleoside triphosphate phosphatase activity / viral capsid / RNA helicase activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / fusion of virus membrane with host endosome membrane ...: / symbiont-mediated transformation of host cell / serine-type peptidase activity / ribonucleoside triphosphate phosphatase activity / viral capsid / RNA helicase activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / proteolysis / ATP binding / membrane
Similarity search - Function
RNA Helicase; Chain A, domain 3 / RNA Helicase Chain A , domain 3 / : / NS3 RNA helicase, C-terminal helical domain / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain ...RNA Helicase; Chain A, domain 3 / RNA Helicase Chain A , domain 3 / : / NS3 RNA helicase, C-terminal helical domain / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-3VZ / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsDavies, D.R. / Kim, H. / Lorimer, D.
CitationJournal: TO BE PUBLISHED
Title: crystal structure of NS3 Helicase from HCV with a bound inhibitor
Authors: Buckman, B.O. / Kossen, K. / Misialek, S. / Stevens, S. / Rajagopalan, R. / Ruhmund, D. / Hooi, L. / Snarskaya, N. / Serebryany, V. / Wang, G. / Stoycheva, A. / Nicholas, J.B. / Davies, D.R. ...Authors: Buckman, B.O. / Kossen, K. / Misialek, S. / Stevens, S. / Rajagopalan, R. / Ruhmund, D. / Hooi, L. / Snarskaya, N. / Serebryany, V. / Wang, G. / Stoycheva, A. / Nicholas, J.B. / Davies, D.R. / Brunton, S. / Montalbetti, C. / Weddell, D. / Goodwin, C. / Schonfeld, D. / Mather, O. / Cheng, R. / Blatt, L. / Beigelman, L.
History
DepositionNov 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS3
B: NS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4294
Polymers96,6022
Non-polymers8272
Water3,225179
1
A: NS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7142
Polymers48,3011
Non-polymers4141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7142
Polymers48,3011
Non-polymers4141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.074, 112.776, 99.592
Angle α, β, γ (deg.)90.00, 126.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NS3


Mass: 48300.793 Da / Num. of mol.: 2 / Fragment: UNP residues 180-630 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Production host: Escherichia coli (E. coli) / References: UniProt: A1Z092
#2: Chemical ChemComp-3VZ / {6-(3,5-diaminophenyl)-1-[4-(propan-2-yl)benzyl]-1H-indol-3-yl}acetic acid


Mass: 413.511 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H27N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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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: 2.9 Å3/Da / Density % sol: 57.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 2.0 M NA/K PHOSPHATE (PH 10.5), 186 MM LI2SO4, 100 MM CAPS PH 10.5, VAPOR DIFFUSION, TEMPERATURE 289K
PH range: 10.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: SBC-3 / Detector: CCD / Date: Mar 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→29.7 Å / Num. obs: 38561 / % possible obs: 92.15 % / Redundancy: 2.4 % / Net I/σ(I): 15.12

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HEI

1hei


Resolution: 2.42→29.7 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.867 / SU B: 25.823 / SU ML: 0.273 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.508 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1931 5 %RANDOM
Rwork0.239 ---
obs0.243 38561 91.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20.06 Å2
2---0.41 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.42→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6511 0 62 179 6752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226733
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9759203
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0655858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29423.56250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.075151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2191534
X-RAY DIFFRACTIONr_chiral_restr0.0950.21069
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215090
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6181.54308
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.13926990
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.67832425
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.74.52213
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.42→2.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 145 -
Rwork0.303 2616 -
obs--91.09 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3201-0.340.08651.39560.31320.87830.02990.07010.0202-0.09280.0231-0.0362-0.03950.0134-0.05290.08510.02830.01040.1249-0.01710.0275-20.28173.001910.6775
20.2171-0.0527-0.39980.7812-0.21420.86070.04990.0205-0.0158-0.0055-0.04410.0489-0.0195-0.0439-0.00570.07450.0313-0.0150.1254-0.01640.0622-18.0634-5.654916.3281
32.6921-0.4769-0.92272.51630.92460.45530.0667-0.14530.3194-0.27620.0787-0.3486-0.11750.0662-0.14530.051-0.01920.04180.0169-0.00230.180214.241210.939325.2031
41.91640.4607-1.12720.51950.10060.8344-0.07450.05960.0265-0.11050.0858-0.0427-0.0015-0.0061-0.01130.07930.0585-0.01070.0823-0.00680.12474.61440.461125.6004
50.40480.06040.29680.46750.6691.73050.1258-0.03550.00440.0535-0.0006-0.05990.14590.0146-0.12530.06440.00090.00950.08940.00610.0681-14.6844-3.376143.1515
60.0590.4465-0.02042.1511-0.41272.0718-0.05540.03810.0346-0.12030.01260.08220.1138-0.00160.04280.0720.0282-0.02330.15010.03360.028618.1479-26.28645.7183
70.4926-0.4415-0.15781.41560.22720.7435-0.0402-0.0139-0.0107-0.0756-0.0234-0.0556-0.02080.130.06370.04790.03180.01180.12450.03240.055722.6103-26.080314.8168
81.48830.37630.61730.77670.13860.4727-0.06330.0071-0.1619-0.05690.02630.1532-0.001-0.01020.0370.05080.03480.01760.058200.1277-7.5459-32.746925.7541
90.33950.2137-0.33570.5309-0.51211.61080.05490.0143-0.03820.0596-0.05420.0032-0.05760.0001-0.00070.06310.0251-0.03280.078-0.00880.075317.6046-24.082139.4959
101.8071.8299-2.51342.6442-0.67346.01690.2942-0.21790.06820.1339-0.24630.2412-0.80460.0444-0.04790.15980.0366-0.00140.08690.02350.082314.7338-15.247449.3469
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A190 - 276
2X-RAY DIFFRACTION2A277 - 330
3X-RAY DIFFRACTION3A331 - 405
4X-RAY DIFFRACTION4A406 - 487
5X-RAY DIFFRACTION5A488 - 627
6X-RAY DIFFRACTION6B186 - 246
7X-RAY DIFFRACTION7B249 - 328
8X-RAY DIFFRACTION8B329 - 480
9X-RAY DIFFRACTION9B481 - 601
10X-RAY DIFFRACTION10B602 - 629

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