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- PDB-2pn3: Crystal Structure of Hepatitis C Virus IRES Subdomain IIa -

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Basic information

Entry
Database: PDB / ID: 2pn3
TitleCrystal Structure of Hepatitis C Virus IRES Subdomain IIa
Components
  • 5'-R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP*AP*CP*GP*CP*C)-3'
  • 5'-R(*GP*CP*GP*(5BU)P*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*(5BU)P*CP*CP*GP*G)-3'
KeywordsRNA / HCV / IRES / Loop IIa / Magnesium / Crystallization
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsZhao, Q. / Han, Q. / Kissinger, C.R. / Hermann, T. / Thompson, P.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structure of hepatitis C virus IRES subdomain IIa.
Authors: Zhao, Q. / Han, Q. / Kissinger, C.R. / Hermann, T. / Thompson, P.A.
History
DepositionApr 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP*AP*CP*GP*CP*C)-3'
B: 5'-R(*GP*CP*GP*(5BU)P*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*(5BU)P*CP*CP*GP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2584
Polymers14,2092
Non-polymers492
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-23.8 kcal/mol
Surface area7620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.945, 48.945, 120.942
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: RNA chain 5'-R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP*AP*CP*GP*CP*C)-3'


Mass: 7644.589 Da / Num. of mol.: 1 / Fragment: HCV IRES Subdomain IIa (residue 47-70) / Mutation: G47C, U48G, A70C / Source method: obtained synthetically
Details: This sequence occurs naturally in hepatitis C virus
#2: RNA chain 5'-R(*GP*CP*GP*(5BU)P*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*(5BU)P*CP*CP*GP*G)-3'


Mass: 6564.623 Da / Num. of mol.: 1 / Fragment: HCV IRES Subdomain IIa (residue 98-117) / Mutation: A99C, A116G / Source method: obtained synthetically
Details: This sequence occurs naturally in hepatitis C virus
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 290 K / Method: evaporation / pH: 6.2
Details: 5% MPD, 5mM MgSO4, 12.5mM NaCl, 50mM KCl, 25mM Cacodylate equilibrated with 65%MPD, pH 6.2, EVAPORATION, temperature 290.0K
Components of the solutions
IDNameCrystal-IDSol-ID
15% MPD11
2MgSO411
3NaCl11
4KCl11
5Cacodylate11
665% MPD12

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.9203, 0.9197, 0.90686
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 30, 2004 / Details: mirrors
RadiationMonochromator: double-crystal Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.92031
20.91971
30.906861
ReflectionResolution: 2.9→50 Å / Num. all: 3650 / Num. obs: 3420 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 55.3 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 27.5
Reflection shellResolution: 2.9→3 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 4.6 / Num. unique all: 253 / % possible all: 75.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
APSBioCARS developed GUIdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→45 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.843 / SU B: 18.57 / SU ML: 0.349 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.46 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28263 143 4.3 %RANDOM
Rwork0.2288 ---
all0.23204 3452 --
obs0.22969 3202 92.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.297 Å2
Baniso -1Baniso -2Baniso -3
1--2.08 Å20 Å20 Å2
2---2.08 Å20 Å2
3---4.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.9→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 930 2 0 932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0211036
X-RAY DIFFRACTIONr_angle_refined_deg1.88531612
X-RAY DIFFRACTIONr_chiral_restr0.0710.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02452
X-RAY DIFFRACTIONr_nbd_refined0.1950.2405
X-RAY DIFFRACTIONr_nbtor_refined0.2990.2673
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.233
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3050.22
X-RAY DIFFRACTIONr_scbond_it1.17731470
X-RAY DIFFRACTIONr_scangle_it2.0064.51612
LS refinement shellResolution: 2.9→2.977 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 9 -
Rwork0.356 169 -
obs-253 70.63 %

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