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

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Basic information

Entry
Database: PDB / ID: 3dvv
TitleCrystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin (U267OMe)
ComponentsHIV-1 genomic RNA
KeywordsRNA / HIV-1 / antibiotic / aminoglycoside
Function / homology: / RIBOSTAMYCIN / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEnnifar, E. / Dumas, P. / Olieric, V.
CitationJournal: To be Published
Title: A fast strategy for Selenium derivatization and phasing of RNA structures
Authors: Olieric, V. / Rieder, U. / Lang, K. / Serganov, A. / Schulze-Brise, C. / Micura, R. / Dumas, P. / Ennifar, E.
History
DepositionJul 21, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 12, 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.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_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 genomic RNA
B: HIV-1 genomic RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9029
Polymers14,8012
Non-polymers1,1017
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint1 kcal/mol
Surface area8360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.703, 30.489, 58.004
Angle α, β, γ (deg.)90.00, 122.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain HIV-1 genomic RNA


Mass: 7400.499 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical
ChemComp-K / POTASSIUM ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-RIO / RIBOSTAMYCIN / 5-AMINO-2-AMINOMETHYL-6-[4,6-DIAMINO-2-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YLOXY)-3-HYDROXY-CYCLOHEXYLOXY ]-TETRAHYDRO-PYRAN-3,4-DIOL / (1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-(beta-D-ribofuranosyloxy)cyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside / Ribostamycin


Mass: 454.473 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H34N4O10 / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 310 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: MPD, cacodylate, MgCl2, KCl, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 310K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2cacodylateCacodylic acid11
3MgCl211
4KCl11
5MPD12
6cacodylate'12
7MgCl212
8KCl12

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 10096 / Num. obs: 9829 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 47.6 Å2 / Rsym value: 0.058 / Net I/σ(I): 29
Reflection shellResolution: 2→2.07 Å / Redundancy: 8 % / Mean I/σ(I) obs: 9.8 / Num. unique all: 971 / Rsym value: 0.309 / % possible all: 91.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3C3Z

3c3z


Resolution: 2→18.59 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 741857.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.277 795 8.1 %RANDOM
Rwork0.268 ---
obs0.268 9635 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.979 Å2 / ksol: 0.358534 e/Å3
Displacement parametersBiso mean: 45.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.14 Å20 Å21.36 Å2
2--14.78 Å20 Å2
3----12.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2→18.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 980 67 44 1091
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d12.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d5.59
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.417 121 7.5 %
Rwork0.425 1488 -
obs--96.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1water_rep.paramwater.top
X-RAY DIFFRACTION2luc.paramdna-rna.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4OMU_xplor.paramOMU_xplor.top
X-RAY DIFFRACTION5ribostamycine.paramribostamycine.top

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