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- PDB-1jzv: Crystal structure of a bulged RNA from the SL2 stem-loop of the H... -

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Basic information

Entry
Database: PDB / ID: 1jzv
TitleCrystal structure of a bulged RNA from the SL2 stem-loop of the HIV-1 psi-RNA
Components
  • 5'-R(*CP*AP*GP*UP*AP*CP*GP*(5IC)P*C)-3'
  • 5'-R(*GP*GP*CP*GP*AP*CP*(5BU)P*G)-3'
KeywordsRNA / A-bulge / A-RNA / HIV-1 SL2
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsXiong, Y. / Sudarsanakumar, C. / Deng, J. / Pan, B. / Sundaralingam, M.
CitationJournal: To be Published
Title: Crystal Structure of a Bulged RNA from the SL2 Stem-loop of the HIV-1 psi-RNA
Authors: Xiong, Y. / Sudarsanakumar, C. / Deng, J. / Pan, M. / Sundaralingam, M.
History
DepositionSep 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

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Assembly

Deposited unit
A: 5'-R(*GP*GP*CP*GP*AP*CP*(5BU)P*G)-3'
B: 5'-R(*CP*AP*GP*UP*AP*CP*GP*(5IC)P*C)-3'
C: 5'-R(*GP*GP*CP*GP*AP*CP*(5BU)P*G)-3'
D: 5'-R(*CP*AP*GP*UP*AP*CP*GP*(5IC)P*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2595
Polymers11,2344
Non-polymers241
Water1,45981
1
A: 5'-R(*GP*GP*CP*GP*AP*CP*(5BU)P*G)-3'
B: 5'-R(*CP*AP*GP*UP*AP*CP*GP*(5IC)P*C)-3'


Theoretical massNumber of molelcules
Total (without water)5,6172
Polymers5,6172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-R(*GP*GP*CP*GP*AP*CP*(5BU)P*G)-3'
D: 5'-R(*CP*AP*GP*UP*AP*CP*GP*(5IC)P*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6413
Polymers5,6172
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.800, 45.800, 89.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 2660.497 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Solid phase phosphoramidite synthesis
#2: RNA chain 5'-R(*CP*AP*GP*UP*AP*CP*GP*(5IC)P*C)-3'


Mass: 2956.655 Da / Num. of mol.: 2 / Source method: obtained synthetically
#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.: 81 / 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: 2.09 Å3/Da / Density % sol: 41.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MPD, magnesium chloride, cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2MgCl212
3cacodylateCacodylic acid13

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9195 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9195 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 19682 / % possible obs: 98 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.063

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.7→20 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1847 9.4 %Random
Rwork0.203 ---
all-20028 --
obs-19558 --
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 718 1 81 800
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.38

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