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- PDB-5une: Dimerized Structure Gives Further Insight Into the Function of th... -

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Basic information

Entry
Database: PDB / ID: 5une
TitleDimerized Structure Gives Further Insight Into the Function of the Novel RNA Gene: HAR1
ComponentsRNA (47-MER)
KeywordsRNA / HAR1 RNA / RNA gene
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.90009915777 Å
AuthorsLares, M. / Scott, W.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM087721 United States
CitationJournal: To Be Published
Title: Dimerized Structure Gives Further Insight Into the Function of the Novel RNA Gene: HAR1
Authors: Lares, M. / Scott, W.G. / Kimberly, T.
History
DepositionJan 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 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

Downloads & links

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Assembly

Deposited unit
A: RNA (47-MER)
B: RNA (47-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6314
Polymers30,5822
Non-polymers492
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-27 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.562, 39.826, 80.974
Angle α, β, γ (deg.)90.000, 111.829, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: RNA chain RNA (47-MER)


Mass: 15291.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA was prepared by in vitro transcription / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.01 Å3/Da / Density % sol: 59.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 500mM Tris-HCl, 1MKCl, 50mM MgCl2

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.855 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.855 Å / Relative weight: 1
ReflectionResolution: 2.9→75 Å / Num. obs: 8346 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 29.6962517799 Å2 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.086 / Net I/σ(I): 7.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.90009915777→39.0345663005 Å / SU ML: 0.457836040834 / Cross valid method: FREE R-VALUE / σ(F): 1.33965098345 / Phase error: 30.709969478
RfactorNum. reflection% reflection
Rfree0.249418559304 812 9.8340801744 %
Rwork0.200532555588 --
obs0.205628872665 8257 98.8980716253 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 28.4610026251 Å2
Refinement stepCycle: LAST / Resolution: 2.90009915777→39.0345663005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2032 2 15 2049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006405179235242276
X-RAY DIFFRACTIONf_angle_d1.182705822973550
X-RAY DIFFRACTIONf_chiral_restr0.0422079448283470
X-RAY DIFFRACTIONf_plane_restr0.0055239858533994
X-RAY DIFFRACTIONf_dihedral_angle_d10.65773450171122
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.08170.3938976754321360.3252155837711241X-RAY DIFFRACTION99.2074927954
3.0817-3.31960.3496874386981200.2579525616171198X-RAY DIFFRACTION96.4155084126
3.3196-3.65340.2647954441891460.200255019791216X-RAY DIFFRACTION99.3435448578
3.6534-4.18150.2173669291671340.1629984097961221X-RAY DIFFRACTION98.9051094891
4.1815-5.26620.1824428475351260.1549755020571267X-RAY DIFFRACTION99.8566308244
5.2662-39.03810.2186428998021500.1841556331891302X-RAY DIFFRACTION99.6568291009

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