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- PDB-2qek: HIV-1 subtype F DIS RNA extended duplex form -

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Basic information

Entry
Database: PDB / ID: 2qek
TitleHIV-1 subtype F DIS RNA extended duplex form
ComponentsHIV-1 subtype F DIS genomic RNA
KeywordsRNA / HIV RNA Bulged-adenine
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFreisz, S. / Ennifar, E. / Dumas, P.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2008
Title: Binding of aminoglycoside antibiotics to the duplex form of the HIV-1 genomic RNA dimerization initiation site.
Authors: Freisz, S. / Lang, K. / Micura, R. / Dumas, P. / Ennifar, E.
History
DepositionJun 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-1 subtype F DIS genomic RNA
B: HIV-1 subtype F DIS genomic RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9156
Polymers14,7732
Non-polymers1424
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-8 kcal/mol
Surface area8410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.773, 37.355, 44.965
Angle α, β, γ (deg.)90.00, 111.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain HIV-1 subtype F DIS genomic RNA


Mass: 7386.472 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in HIV-1 subtype F
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 310 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: MPD, MgCl2, KCl, Na cacodylate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 310K
Components of the solutions
IDNameCrystal-IDSol-ID
1Na cacodylate11
2MPD11
3MgCl211
4KCl11
5MPD12
6MgCl212
7KCl12

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2007 / Details: crystal
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 24846 / Num. obs: 24275 / % possible obs: 0.977 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.063 / Net I/σ(I): 19.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5 % / Mean I/σ(I) obs: 6.6 / Num. unique all: 2472 / Rsym value: 0.35 / % possible all: 0.998

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Processing

Software
NameVersionClassification
MXCUBEdata collection
CNSrefinement
DENZOdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Y99

1y99


Resolution: 1.8→21.69 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 558620.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.265 941 7.9 %RANDOM
Rwork0.251 ---
all0.2511 12733 --
obs0.2511 11842 93 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.0178 Å2 / ksol: 0.372645 e/Å3
Displacement parametersBiso mean: 39.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å2-2.44 Å2
2---1.2 Å20 Å2
3---1.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.8→21.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 978 4 73 1055
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d8.1
X-RAY DIFFRACTIONc_improper_angle_d1.34
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 149 8.4 %
Rwork0.272 1629 -
obs--84.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1luc.paramdna-rna.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top

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