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- PDB-1y99: HIV-1 subtype A DIS RNA duplex -

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Basic information

Entry
Database: PDB / ID: 1y99
TitleHIV-1 subtype A DIS RNA duplex
Components5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3'
KeywordsRNA / HIV-1 / bulge / magnesium
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsEnnifar, E. / Yusupov, M. / Walter, P. / Marquet, R. / Ehresmann, B. / Ehresmann, C. / Dumas, P.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges
Authors: Ennifar, E. / Yusupov, M. / Walter, P. / Marquet, R. / Ehresmann, B. / Ehresmann, C. / Dumas, P.
History
DepositionDec 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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: 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3'
B: 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9759
Polymers14,8052
Non-polymers1707
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.698, 31.422, 51.188
Angle α, β, γ (deg.)90.00, 115.82, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11B-127-

HOH

21B-169-

HOH

31B-176-

HOH

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Components

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


Mass: 7402.472 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: HIV-1 DIS RNA
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.23 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 310 K / Method: vapor diffusion, sitting drop / pH: 7
Details: MPD, spermine, KCl, MgCl2, Na Cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 310K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2spermine11
3KCl11
4MgCl211
5Na Cacodylate11
6H2O11
7MPD12
8KCl12
9MgCl212
10Na Cacodylate12

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.9615 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 19, 1999
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9615 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. all: 6799 / Num. obs: 6534 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 65.4 Å2 / Rsym value: 0.032
Reflection shellResolution: 2.2→2.28 Å / Rsym value: 0.351 / % possible all: 85.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 462D

462d


Resolution: 2.4→9.97 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 605002.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 519 10.4 %RANDOM
Rwork0.225 ---
obs0.225 5001 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.8383 Å2 / ksol: 0.287313 e/Å3
Displacement parametersBiso mean: 40.1 Å2
Baniso -1Baniso -2Baniso -3
1--8.13 Å20 Å2-0.63 Å2
2--13.52 Å20 Å2
3----5.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.4→9.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1048 7 82 1137
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
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_deg0.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d10
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.23
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.171.5
X-RAY DIFFRACTIONc_mcangle_it3.152
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.053 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.464 76 10.4 %
Rwork0.395 653 -
obs--85.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION2DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4BRU_REP.PARAM

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