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- PDB-1csl: CRYSTAL STRUCTURE OF THE RRE HIGH AFFINITY SITE -

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Basic information

Entry
Database: PDB / ID: 1csl
TitleCRYSTAL STRUCTURE OF THE RRE HIGH AFFINITY SITE
Components
  • 5'-R(*AP*AP*CP*GP*GP*GP*CP*GP*CP*AP*GP*AP*A)-3'
  • 5'-R(*UP*CP*UP*GP*AP*CP*GP*GP*UP*AP*CP*GP*UP*UP*U)-3'
KeywordsRNA / RRE HIGH AFFINITY SITE / HIV-1
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsIppolito, J.A. / Steitz, T.A.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The structure of the HIV-1 RRE high affinity rev binding site at 1.6 A resolution.
Authors: Ippolito, J.A. / Steitz, T.A.
History
DepositionAug 18, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 28, 2011Group: Advisory
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*AP*AP*CP*GP*GP*GP*CP*GP*CP*AP*GP*AP*A)-3'
B: 5'-R(*UP*CP*UP*GP*AP*CP*GP*GP*UP*AP*CP*GP*UP*UP*U)-3'


Theoretical massNumber of molelcules
Total (without water)8,9892
Polymers8,9892
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.5, 24.3, 46.1
Angle α, β, γ (deg.)90, 116.7, 90
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

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


Mass: 4242.646 Da / Num. of mol.: 1 / Fragment: HIGH AFFINITY REV BINDING SITE / Source method: obtained synthetically / Details: SEQUENCE NATURALLY OCCURS IN RRE OF HIV-1
#2: RNA chain 5'-R(*UP*CP*UP*GP*AP*CP*GP*GP*UP*AP*CP*GP*UP*UP*U)-3'


Mass: 4746.817 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: LITHIUM SULFATE, MAGNESIUM SULFATE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1LI2SO411
2MGSO411
3SODIUM CACODYLATE11
Crystal grow
*PLUS
Method: vapor diffusion
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMprotein1drop
21.8 M1reservoirLi2SO4
310 mM1reservoirMgSO4
450 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 9, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 9651 / Num. obs: 9651 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 17.6
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 3.4 / % possible all: 81
Reflection
*PLUS
Num. measured all: 30269
Reflection shell
*PLUS
% possible obs: 81 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→15 Å / Rfactor Rfree error: 0.008 / Data cutoff high rms absF: 17752510.83 / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: PARKINSON ET AL., ACTA CRYST. D, 52 (1996) 57-64
RfactorNum. reflection% reflectionSelection details
Rfree0.241 993 10 %RANDOM
Rwork0.211 ---
obs0.211 9640 96.3 %-
all-9640 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.4733 Å2 / ksol: 0.411304 e/Å3
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å2-0.83 Å2
2--0.35 Å20 Å2
3---1.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-15 Å
Luzzati sigma a0.18 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 595 0 144 739
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d29.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.99
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.151.5
X-RAY DIFFRACTIONc_mcangle_it0.262
X-RAY DIFFRACTIONc_scbond_it0.082
X-RAY DIFFRACTIONc_scangle_it0.142.5
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.272 69 8.7 %
Rwork0.295 723 -
obs--81.2 %
Xplor fileSerial no: 1 / Param file: DNA-RNA-MULTI-ENDO.PARAM / Topol file: DNA-RNA-MULTI-ENDO.TOP
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg29.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.99

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