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- PDB-2grb: Crystal Structure of an RNA Quadruplex Containing Inosine-tetrad -

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Basic information

Entry
Database: PDB / ID: 2grb
TitleCrystal Structure of an RNA Quadruplex Containing Inosine-tetrad
Components5'-R(*(U33)P*GP*IP*GP*GP*U)-3'
KeywordsRNA / RNA Quadruplex
Function / homology: / STRONTIUM ION / RNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsPan, B. / Shi, K. / Sundaralingam, M.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal structure of an RNA quadruplex containing inosine tetrad: implications for the roles of NH2 group in purine tetrads.
Authors: Pan, B. / Shi, K. / Sundaralingam, M.
History
DepositionApr 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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_conn_type / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_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.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.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_type.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(*(U33)P*GP*IP*GP*GP*U)-3'
B: 5'-R(*(U33)P*GP*IP*GP*GP*U)-3'
C: 5'-R(*(U33)P*GP*IP*GP*GP*U)-3'
D: 5'-R(*(U33)P*GP*IP*GP*GP*U)-3'
E: 5'-R(*(U33)P*GP*IP*GP*GP*U)-3'
F: 5'-R(*(U33)P*GP*IP*GP*GP*U)-3'
G: 5'-R(*(U33)P*GP*IP*GP*GP*U)-3'
H: 5'-R(*(U33)P*GP*IP*GP*GP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,84620
Polymers15,3298
Non-polymers51812
Water3,207178
1
A: 5'-R(*(U33)P*GP*IP*GP*GP*U)-3'
B: 5'-R(*(U33)P*GP*IP*GP*GP*U)-3'
C: 5'-R(*(U33)P*GP*IP*GP*GP*U)-3'
D: 5'-R(*(U33)P*GP*IP*GP*GP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,94810
Polymers7,6644
Non-polymers2836
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: 5'-R(*(U33)P*GP*IP*GP*GP*U)-3'
F: 5'-R(*(U33)P*GP*IP*GP*GP*U)-3'
G: 5'-R(*(U33)P*GP*IP*GP*GP*U)-3'
H: 5'-R(*(U33)P*GP*IP*GP*GP*U)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,89910
Polymers7,6644
Non-polymers2356
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.060, 52.738, 37.344
Angle α, β, γ (deg.)90.00, 102.98, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is one tetramer (e.g. chain A, B, C, D), half of the asymmetric unit.

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Components

#1: RNA chain
5'-R(*(U33)P*GP*IP*GP*GP*U)-3'


Mass: 1916.099 Da / Num. of mol.: 8 / Source method: obtained synthetically
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Sr
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 1.82 Å3/Da / Density % sol: 32.38 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7
Details: KCl, CaCl2, MPD , pH 7.0, EVAPORATION, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1KCl11
2CaCl211
3MPD11
4H2O11
5KCl12
6CaCl212
7MPD12

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9195,0.9200,0.8984
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 9, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91951
20.921
30.89841
ReflectionResolution: 1.4→30 Å / Num. obs: 23152 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.87 %
Reflection shellResolution: 1.4→1.45 Å / % possible all: 71.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
d*TREKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→8 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.136 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25002 1006 4.9 %RANDOM
Rwork0.19514 ---
all0.19781 19509 --
obs0.19781 19509 95.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.058 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å2-1.66 Å2
2---2.35 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 970 12 178 1160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211069
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7831647
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.2910.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02497
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3510.2451
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2650.2636
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2540.2170
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1760.253
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.233
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2830.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it2.48831135
X-RAY DIFFRACTIONr_scangle_it3.074.51647
X-RAY DIFFRACTIONr_rigid_bond_restr1.96931135
X-RAY DIFFRACTIONr_sphericity_free3.5073217
X-RAY DIFFRACTIONr_sphericity_bonded3.4363959
LS refinement shellResolution: 1.4→1.435 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 47 -
Rwork0.397 1011 -
obs--69.2 %

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