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- PDB-1j6s: Crystal Structure of an RNA Tetraplex (UGAGGU)4 with A-tetrads, G... -

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Basic information

Entry
Database: PDB / ID: 1j6s
TitleCrystal Structure of an RNA Tetraplex (UGAGGU)4 with A-tetrads, G-tetrads, U-tetrads and G-U octads
Components5'-R(*(BRUP*GP*AP*GP*GP*U)-3'
KeywordsRNA / Tetraplex / G-U octads / A-tetrads / U-tetrads / G-tetrads
Function / homology: / RNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsPan, B. / Xiong, Y. / Shi, K. / Deng, J. / Sundaralingam, M.
CitationJournal: Structure / Year: 2003
Title: Crystal structure of an RNA purine-rich tetraplex containing adenine tetrads: implications for specific binding in RNA tetraplexes
Authors: Pan, B. / Xiong, Y. / Shi, K. / Deng, J. / Sundaralingam, M.
History
DepositionJul 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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 / _struct_conn.conn_type_id / _struct_conn.id / _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.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

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Assembly

Deposited unit
A: 5'-R(*(BRUP*GP*AP*GP*GP*U)-3'
B: 5'-R(*(BRUP*GP*AP*GP*GP*U)-3'
C: 5'-R(*(BRUP*GP*AP*GP*GP*U)-3'
D: 5'-R(*(BRUP*GP*AP*GP*GP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,26320
Polymers7,9804
Non-polymers1,28316
Water2,036113
1
A: 5'-R(*(BRUP*GP*AP*GP*GP*U)-3'
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)9,26320
Polymers7,9804
Non-polymers1,28316
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(*(BRUP*GP*AP*GP*GP*U)-3'
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)9,26320
Polymers7,9804
Non-polymers1,28316
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(*(BRUP*GP*AP*GP*GP*U)-3'
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)9,35524
Polymers7,9804
Non-polymers1,37420
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
4
D: 5'-R(*(BRUP*GP*AP*GP*GP*U)-3'
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)9,17116
Polymers7,9804
Non-polymers1,19112
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)37.984, 37.984, 82.195
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-105-

BA

21A-108-

BA

31A-205-

NA

41A-206-

NA

51B-103-

BA

61B-104-

BA

71B-202-

NA

81B-207-

NA

91C-101-

BA

101C-201-

NA

111C-203-

NA

121C-209-

NA

131D-102-

BA

141D-107-

BA

151D-208-

NA

161A-387-

HOH

171D-320-

HOH

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Components

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


Mass: 1995.094 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ba
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 1.86 Å3/Da / Density % sol: 33.78 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11 mMRNA1drop
220 mMsodium cacodylate1droppH6.0
390 mM1dropNaCl
410 mM1dropBaCl2
56 mMspermine tetrahydrochloride1drop
62 %(v/v)MPD1drop
715 %MPD1reservoir

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 22622 / Num. obs: 22556
Reflection
*PLUS
Highest resolution: 1.4 Å / Num. obs: 22704 / % possible obs: 99.9 % / Num. measured all: 572671 / Rmerge(I) obs: 0.067

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Processing

Software
NameVersionClassification
DENZOdata reduction
SOLVEphasing
RESOLVEmodel building
CNS1.1refinement
RESOLVEphasing
RefinementResolution: 1.4→30 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.184 1087 4.8 %
Rwork0.166 --
obs-22556 99.4 %
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 496 16 113 625
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg2
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1ion.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param

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