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- PDB-1j8g: X-ray Analysis of a RNA Tetraplex r(uggggu)4 at Ultra-High Resolution -

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Basic information

Entry
Database: PDB / ID: 1j8g
TitleX-ray Analysis of a RNA Tetraplex r(uggggu)4 at Ultra-High Resolution
Components5'-R(*UP*GP*GP*GP*GP*U)-3'
KeywordsRNA / RNA tetraplex / Sr ions / U tetrad / Octaplex
Function / homologySPERMINE / STRONTIUM ION / RNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 0.61 Å
AuthorsDeng, J. / Xiong, Y. / Sundaralingam, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: X-ray analysis of an RNA tetraplex (UGGGGU)(4) with divalent Sr(2+) ions at subatomic resolution (0.61 A).
Authors: Deng, J. / Xiong, Y. / Sundaralingam, M.
History
DepositionMay 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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(*UP*GP*GP*GP*GP*U)-3'
B: 5'-R(*UP*GP*GP*GP*GP*U)-3'
C: 5'-R(*UP*GP*GP*GP*GP*U)-3'
D: 5'-R(*UP*GP*GP*GP*GP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,86218
Polymers7,7934
Non-polymers1,07014
Water1,910106
1
A: 5'-R(*UP*GP*GP*GP*GP*U)-3'
hetero molecules

A: 5'-R(*UP*GP*GP*GP*GP*U)-3'
hetero molecules

A: 5'-R(*UP*GP*GP*GP*GP*U)-3'
hetero molecules

A: 5'-R(*UP*GP*GP*GP*GP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,55524
Polymers7,7934
Non-polymers1,76320
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
2
B: 5'-R(*UP*GP*GP*GP*GP*U)-3'
hetero molecules

B: 5'-R(*UP*GP*GP*GP*GP*U)-3'
hetero molecules

B: 5'-R(*UP*GP*GP*GP*GP*U)-3'
hetero molecules

B: 5'-R(*UP*GP*GP*GP*GP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,74620
Polymers7,7934
Non-polymers95316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_655-y+3/2,x+1/2,z1
crystal symmetry operation4_465y-1/2,-x+3/2,z1
3
C: 5'-R(*UP*GP*GP*GP*GP*U)-3'
hetero molecules

C: 5'-R(*UP*GP*GP*GP*GP*U)-3'
hetero molecules

C: 5'-R(*UP*GP*GP*GP*GP*U)-3'
hetero molecules

C: 5'-R(*UP*GP*GP*GP*GP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,65416
Polymers7,7934
Non-polymers86112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
4
D: 5'-R(*UP*GP*GP*GP*GP*U)-3'
hetero molecules

D: 5'-R(*UP*GP*GP*GP*GP*U)-3'
hetero molecules

D: 5'-R(*UP*GP*GP*GP*GP*U)-3'
hetero molecules

D: 5'-R(*UP*GP*GP*GP*GP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,49412
Polymers7,7934
Non-polymers7018
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-x+1,-y+2,z1
crystal symmetry operation3_655-y+3/2,x+1/2,z1
crystal symmetry operation4_465y-1/2,-x+3/2,z1
Unit cell
Length a, b, c (Å)36.154, 36.154, 74.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-505-

SR

21A-506-

SR

31A-512-

NA

41B-502-

SR

51B-507-

SR

61B-513-

NA

71C-503-

SR

81C-504-

SR

91D-501-

SR

101D-508-

SR

111B-101-

HOH

121C-102-

HOH

131D-131-

HOH

141D-178-

HOH

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Components

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RNA chain , 1 types, 4 molecules ABCD

#1: RNA chain
5'-R(*UP*GP*GP*GP*GP*U)-3'


Mass: 1948.197 Da / Num. of mol.: 4 / Source method: obtained synthetically

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Non-polymers , 5 types, 120 molecules

#2: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#3: Chemical
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Sr
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 1.55 Å3/Da / Density % sol: 20.87 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: 20mM Sodium Cacodylate (pH 7.0), 12mM spermine tetrachloride, 20mM MgCl2, 80mM SrCl2, 40mM CaCl2, 35% MPD, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1Sodium Cacodylate11
2spermine tetrachloride11
3MgCl211
4SrCl211
5CaCl211
6MPD11
Crystal grow
*PLUS
Temperature: 293 K
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
140 mMsodium cacodylate1droppH7.0
220 mM1dropMgCl2
312.0 mMspermine chloride1drop
480 mM1dropLiCl
540 mM1dropSrCl2
620 mM1dropCaCl2
710 %(v/v)MPD1drop
835 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.8 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.61→20 Å / Num. obs: 207845 / % possible obs: 92.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 26
Reflection shellResolution: 0.61→0.62 Å / Rmerge(I) obs: 0.339 / % possible all: 61.5
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 61.5 % / Mean I/σ(I) obs: 2

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Processing

Software
NameClassification
MLPHAREphasing
SHELXL-97refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 0.61→20 Å
RfactorNum. reflectionSelection details
Rfree0.112 10452 Thin Cell
Rwork0.103 --
obs-207845 -
Refinement stepCycle: LAST / Resolution: 0.61→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 516 31 127 674
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.1032 / Rfactor Rfree: 0.1117
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_mcbond_it
X-RAY DIFFRACTIONs_scbond_it
X-RAY DIFFRACTIONs_mcangle_it
X-RAY DIFFRACTIONs_scangle_it

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