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- PDB-5xwg: Crystal structure of a novel RNA motif that allows for precise po... -

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Basic information

Entry
Database: PDB / ID: 5xwg
TitleCrystal structure of a novel RNA motif that allows for precise positioning of a metal ion
ComponentsRNA (5'-R(P*CP*GP*CP*UP*(5BU)P*CP*GP*AP*AP*AP*AP*AP*GP*UP*C)-3')
KeywordsRNA / metal-ion-binding motif / X-ray analysis
Function / homologySTRONTIUM ION / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.002 Å
AuthorsKanazawa, H. / Kondo, J.
Funding support Japan, 3items
OrganizationGrant numberCountry
the Ichiro Kanehara Foundation Japan
AMED Japan
the Japan Science Society Japan
CitationJournal: J. Inorg. Biochem. / Year: 2017
Title: Crystal structure of a novel RNA motif that allows for precise positioning of a single metal ion.
Authors: Kanazawa, H. / Kondo, J.
History
DepositionJun 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(P*CP*GP*CP*UP*(5BU)P*CP*GP*AP*AP*AP*AP*AP*GP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1184
Polymers4,8551
Non-polymers2633
Water00
1
A: RNA (5'-R(P*CP*GP*CP*UP*(5BU)P*CP*GP*AP*AP*AP*AP*AP*GP*UP*C)-3')
hetero molecules

A: RNA (5'-R(P*CP*GP*CP*UP*(5BU)P*CP*GP*AP*AP*AP*AP*AP*GP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2358
Polymers9,7102
Non-polymers5266
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_445-x-1,-y-1/2,z1
Buried area3710 Å2
ΔGint-136 kcal/mol
Surface area5440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.544, 80.544, 80.544
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-5-

C

21A-102-

SR

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Components

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


Mass: 4854.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Sr / Feature type: SUBJECT OF INVESTIGATION

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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: 4.48 Å3/Da / Density % sol: 72.57 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: sodium cacodylate, spermine tetrahydrochloride, 2-methyl-2,4-pentanediol, strontium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.91972 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91972 Å / Relative weight: 1
ReflectionResolution: 3.002→56.953 Å / Num. obs: 3373 / % possible obs: 99.6 % / Redundancy: 11.1 % / Biso Wilson estimate: 101.31 Å2 / Net I/σ(I): 19.3
Reflection shellResolution: 3→3.1 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.337 / % possible all: 100

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.22data extraction
CrystalCleardata reduction
AutoSolphasing
RefinementResolution: 3.002→21.526 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 27.89
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2255 305 9.07 %
Rwork0.217 --
obs0.2177 3364 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.06 Å2 / Biso mean: 90.52 Å2 / Biso min: 60.7 Å2
Refinement stepCycle: final / Resolution: 3.002→21.526 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 320 3 0 323
Biso mean--133.35 --
Num. residues----15
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014379
X-RAY DIFFRACTIONf_angle_d1.439588
X-RAY DIFFRACTIONf_chiral_restr0.16379
X-RAY DIFFRACTIONf_plane_restr0.02516
X-RAY DIFFRACTIONf_dihedral_angle_d9.368183
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0017-3.77850.21321240.225915471671100
3.7785-21.52690.22811810.21451512169399

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