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- PDB-4rne: Structural variations and solvent structure of UGGGGU quadruplexe... -

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Basic information

Entry
Database: PDB / ID: 4rne
TitleStructural variations and solvent structure of UGGGGU quadruplexes stabilized by Sr2+ ions
ComponentsRNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
KeywordsRNA / RNA quadruplexes / parallel-stranded
Function / homologySTRONTIUM ION / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.01 Å
AuthorsFyfe, A.C. / Dunten, P.W. / Scott, W.G.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structural Variations and Solvent Structure of r(UGGGGU) Quadruplexes Stabilized by Sr(2+) Ions.
Authors: Fyfe, A.C. / Dunten, P.W. / Martick, M.M. / Scott, W.G.
History
DepositionOct 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Feb 28, 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.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.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.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(*UP*GP*GP*GP*GP*U)-3')
B: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
C: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
D: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
E: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
F: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
G: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
H: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,61227
Polymers15,5868
Non-polymers1,02619
Water4,179232
1
A: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
B: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
C: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
D: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
hetero molecules

A: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
B: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
C: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
D: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,42926
Polymers15,5868
Non-polymers84318
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area8500 Å2
ΔGint-87 kcal/mol
Surface area4080 Å2
MethodPISA
2
E: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
F: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
G: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
H: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
hetero molecules

E: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
F: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
G: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
H: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,79428
Polymers15,5868
Non-polymers1,20920
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area8420 Å2
ΔGint-84 kcal/mol
Surface area4210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.656, 54.197, 95.677
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11E-601-

SR

21E-602-

SR

31F-701-

NA

41G-801-

SR

51G-802-

SR

61D-9521-

HOH

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Components

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


Mass: 1948.197 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: RNA UGGGGU quadruplexes / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Sr
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 1.56 Å3/Da / Density % sol: 21.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: MgCl2 20mM, SrCl2 80mM, CaCl2 40mM, SPM 4Cl 12mM, Sodium cacodylate 20mM, 35% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.01→95.68 Å / Num. all: 51294 / Num. obs: 51294 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.01→1.06 Å / Num. unique all: 7088 / % possible all: 94.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASERphasing
REFMAC5.8.0073refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.01→28 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.985 / SU B: 0.578 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.11916 2606 5.1 %RANDOM
Rwork0.10185 ---
obs0.10275 48629 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.816 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0 Å2
2---0.08 Å2-0 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.01→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1032 19 232 1283
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0111215
X-RAY DIFFRACTIONr_bond_other_d0.0020.02416
X-RAY DIFFRACTIONr_angle_refined_deg1.671.2471894
X-RAY DIFFRACTIONr_angle_other_deg1.74731016
X-RAY DIFFRACTIONr_chiral_restr0.10.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0430.02558
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02160
X-RAY DIFFRACTIONr_scbond_it1.4631214
X-RAY DIFFRACTIONr_scbond_other1.3041192
X-RAY DIFFRACTIONr_scangle_other1.7591863
X-RAY DIFFRACTIONr_long_range_B_refined3.0412339
X-RAY DIFFRACTIONr_long_range_B_other2.322149
X-RAY DIFFRACTIONr_rigid_bond_restr6.44931032
X-RAY DIFFRACTIONr_sphericity_free24.249624
X-RAY DIFFRACTIONr_sphericity_bonded10.25261157
LS refinement shellResolution: 1.01→1.036 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 169 -
Rwork0.291 3256 -
obs--90.73 %

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