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- PDB-6n5t: Structure of Human pir-miRNA-378a Apical Loop Fused to the YdaO R... -

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Basic information

Entry
Database: PDB / ID: 6n5t
TitleStructure of Human pir-miRNA-378a Apical Loop Fused to the YdaO Riboswitch Scaffold
ComponentsRNA (126-MER)
KeywordsRNA / microRNA / RNA processing / Protein-RNA interaction
Function / homologyChem-2BA / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.787 Å
AuthorsShoffner, G.M. / Peng, Z. / Guo, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1616265 United States
CitationJournal: To Be Published
Title: Three-dimensional structures of pri-miRNA apical junctions and loops revealed by scaffold-directed crystallography
Authors: Shoffner, G.M. / Peng, Z. / Guo, F.
History
DepositionNov 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (126-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4559
Polymers40,9061
Non-polymers1,5498
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.810, 113.810, 114.990
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 (126-MER)


Mass: 40906.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)
#2: Chemical ChemComp-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O12P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 5.26 Å3/Da / Density % sol: 76.6 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1.7 M (NH4)2SO4, 0.2 M Li2SO4, and 0.1 M HEPES pH 7.4
Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 20, 2017
RadiationMonochromator: Water-cooled flat double Si(111) Khozu monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2.787→74.834 Å / Num. obs: 21687 / % possible obs: 99.1 % / Redundancy: 20 % / CC1/2: 1 / Rpim(I) all: 0.014 / Rrim(I) all: 0.059 / Net I/σ(I): 27.7
Reflection shellResolution: 2.79→2.89 Å / Redundancy: 17 % / Mean I/σ(I) obs: 2.1 / CC1/2: 0.848 / Rpim(I) all: 0.327 / Rrim(I) all: 1.4 / % possible all: 88.5

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QK8

4qk8


Resolution: 2.787→74.834 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.12
RfactorNum. reflection% reflectionSelection details
Rfree0.1963 2170 10.01 %Random selection
Rwork0.1801 ---
obs0.1818 21687 98.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 313.69 Å2 / Biso mean: 110.1714 Å2 / Biso min: 54.03 Å2
Refinement stepCycle: final / Resolution: 2.787→74.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2705 98 0 2803
Biso mean--70.56 --
Num. residues----126
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7872-2.84780.46611160.45221042115886
2.8478-2.91410.40431330.353212011334100
2.9141-2.98690.32081360.300512211357100
2.9869-3.06770.29531360.261412231359100
3.0677-3.1580.27591360.248312231359100
3.158-3.25990.2831340.248112021336100
3.2599-3.37640.27751360.222912211357100
3.3764-3.51160.25321360.21441211134799
3.5116-3.67140.2211360.22511231136799
3.6714-3.8650.24041340.20031208134299
3.865-4.10710.19911360.183712241360100
4.1071-4.42420.14531350.170112231358100
4.4242-4.86930.17081380.148712451383100
4.8693-5.57370.151410.139412641405100
5.5737-7.02150.14311390.151812551394100
7.0215-74.86120.18081480.15113231471100

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