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- PDB-3c44: Crystal structure of HIV-1 subtype F DIS extended duplex RNA boun... -

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Basic information

Entry
Database: PDB / ID: 3c44
TitleCrystal structure of HIV-1 subtype F DIS extended duplex RNA bound to paromomycin
ComponentsHIV-1 subtype F genomic RNA
KeywordsRNA / HIV-1 / antibiotic / paromomycin / extended duplex
Function / homology: / PAROMOMYCIN / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionJan 29, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 genomic RNA
B: HIV-1 subtype F genomic RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,23110
Polymers14,7732
Non-polymers1,4598
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-71 kcal/mol
Surface area7860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.818, 95.703, 47.856
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-96-

HOH

21B-63-

HOH

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Components

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


Mass: 7386.472 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-PAR / PAROMOMYCIN / PAROMOMYCIN I / AMMINOSIDIN / CATENULIN / CRESTOMYCIN / MONOMYCIN A / NEOMYCIN E


Mass: 615.628 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H45N5O14 / Comment: medication*YM
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.39 Å3/Da / Density % sol: 48.5 %
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
2MgCl211
3KCl11
4MPD11
5Na cacodylate12
6MgCl212
7KCl12
8MPD12

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9195 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 22, 2004
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9195 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 9333 / % possible obs: 92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 24.4 Å2 / Rsym value: 0.049 / Net I/σ(I): 25.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 759 / Rsym value: 0.17 / % possible all: 77.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DNAdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C3Z

3c3z


Resolution: 2→26.55 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 834219.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 762 8.2 %RANDOM
Rwork0.224 ---
obs0.224 9315 92 %-
all-9333 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.5866 Å2 / ksol: 0.444731 e/Å3
Displacement parametersBiso mean: 35.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---0.51 Å20 Å2
3---0.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2→26.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 978 90 139 1207
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d9.5
X-RAY DIFFRACTIONc_improper_angle_d1.39
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.33 108 7.9 %
Rwork0.306 1267 -
obs--83.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1dna-rna_multi_end.paramdna-rna_multi_end.top
X-RAY DIFFRACTION2paromomycine.paramparomomycine.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top
X-RAY DIFFRACTION4ion.paramion.top

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