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- PDB-3ibk: Crystal structure of a telomeric RNA quadruplex -

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Basic information

Entry
Database: PDB / ID: 3ibk
TitleCrystal structure of a telomeric RNA quadruplex
ComponentsRNA (5'-R(*(5BU)P*AP*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3')
KeywordsRNA / rna quadruplex / bimolecular quadruplex / parallel stranded
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCollie, G.W. / Neidle, S. / Parkinson, G.N.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex
Authors: Collie, G.W. / Haider, S.M. / Neidle, S. / Parkinson, G.N.
History
DepositionJul 16, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.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_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: RNA (5'-R(*(5BU)P*AP*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3')
B: RNA (5'-R(*(5BU)P*AP*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,0554
Polymers7,9762
Non-polymers782
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-7 kcal/mol
Surface area4440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.583, 57.583, 38.377
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 3988.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.3 Å3/Da / Density % sol: 46.58 % / Mosaicity: 1.48 °
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MPD, , KCl, NaCl, NaCacodylate, polyamine, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å
DetectorType: OXFORD TITAN CCD / Detector: CCD / Date: Jun 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→49.869 Å / Num. obs: 3912 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rsym value: 0.046
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6 % / Mean I/σ(I) obs: 4.54 / Rsym value: 0.24 / % possible all: 97.3

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
CrysalisProdata collection
CrysalisProdata reduction
REFMAC5.5.0072phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1K8P

1k8p


Resolution: 2.2→11.69 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0 / SU B: 9.78 / SU ML: 0.142 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.231 176 4.5 %RANDOM
Rwork0.215 ---
obs0.216 3899 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 50.12 Å2 / Biso mean: 24.257 Å2 / Biso min: 8.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å20 Å2
2---0.16 Å20 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.2→11.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 520 2 45 567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021497
X-RAY DIFFRACTIONr_angle_refined_deg0.8593774
X-RAY DIFFRACTIONr_chiral_restr0.0580.299
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.02224
X-RAY DIFFRACTIONr_scbond_it2.5553497
X-RAY DIFFRACTIONr_scangle_it3.634.5774
LS refinement shellResolution: 2.2→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 13 -
Rwork0.294 266 -
all-279 -
obs--99.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.9943-2.07260.36274.9998-1.37274.4407-0.0188-0.2550.07830.60390.14610.3743-0.2369-0.2454-0.12720.0476-0.0084-0.00630.0833-0.01740.05522.851825.751538.1223
22.2504-0.4003-0.35584.21292.25761.21880.04770.06410.1474-0.31660.0797-0.1867-0.45790.083-0.12750.0653-0.0005-0.00340.0650.02010.06458.542530.162133.7897
34.0719-1.37180.32590.5588-0.48061.4492-0.16960.9455-0.4775-0.63670.20910.07850.11740.0423-0.03940.1232-0.00030.00480.1060.0040.11069.183518.460328.926
45.13511.72822.54751.4768-1.09325.51430.08030.162-0.6099-0.228-0.06720.31580.3998-0.0236-0.01320.0072-0.01340.01130.00430.0022-0.0057-0.810318.176733.2025
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 6
2X-RAY DIFFRACTION2A7 - 12
3X-RAY DIFFRACTION3B14 - 17
4X-RAY DIFFRACTION4B18 - 24

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