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

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Basic information

Entry
Database: PDB / ID: 4rkv
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: 0.88 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 14, 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_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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,54812
Polymers3,8962
Non-polymers65210
Water97354
1
A: RNA (5'-R(*UP*GP*GP*GP*GP*U)-3')
B: 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')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)18,19348
Polymers15,5868
Non-polymers2,60740
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area8250 Å2
ΔGint-85 kcal/mol
Surface area4400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.645, 36.645, 37.078
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-9001-

SR

21A-9002-

SR

31A-9003-

NA

41B-2101-

SR

51B-2102-

SR

61B-2103-

NA

71A-9116-

HOH

81A-9125-

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.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Sr
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 1.6 Å3/Da / Density % sol: 23 %
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: BL11-1 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 0.88→37.08 Å / Num. all: 19031 / Num. obs: 19031 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 0.88→0.93 Å / % possible all: 58.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASERphasing
REFMAC5.8.0073refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.88→37.08 Å / Cor.coef. Fo:Fc: 0.989 / Cor.coef. Fo:Fc free: 0.989 / SU B: 0.331 / SU ML: 0.009 / Cross valid method: THROUGHOUT / ESU R: 0.013 / ESU R Free: 0.012 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.09811 975 5.1 %RANDOM
Rwork0.09272 ---
obs0.09299 18036 93.31 %-
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: 12.663 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 0.88→37.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 258 10 54 322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.011294
X-RAY DIFFRACTIONr_bond_other_d0.0020.02116
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.248459
X-RAY DIFFRACTIONr_angle_other_deg1.8823287
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_restr0.1060.249
X-RAY DIFFRACTIONr_gen_planes_refined0.0520.02132
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0244
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.079293
X-RAY DIFFRACTIONr_scbond_other1.073292
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.496459
X-RAY DIFFRACTIONr_long_range_B_refined1.939533
X-RAY DIFFRACTIONr_long_range_B_other1.713500
X-RAY DIFFRACTIONr_rigid_bond_restr5.4333284
X-RAY DIFFRACTIONr_sphericity_free22.9216.822
X-RAY DIFFRACTIONr_sphericity_bonded9.6736.8307
LS refinement shellResolution: 0.88→0.907 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 22 -
Rwork0.441 529 -
obs--37.77 %

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