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- PDB-6n5o: Structure of Human pir-miRNA-202 Apical Loop and One-base-pair Fu... -

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Basic information

Entry
Database: PDB / ID: 6n5o
TitleStructure of Human pir-miRNA-202 Apical Loop and One-base-pair 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: 2.708 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)42,4649
Polymers40,9151
Non-polymers1,5498
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.920, 114.920, 115.330
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain RNA (126-MER)


Mass: 40915.195 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)

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Non-polymers , 5 types, 12 molecules

#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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 5.37 Å3/Da / Density % sol: 77.11 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1.9 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: APS / Beamline: 24-ID-C / Wavelength: 0.9202 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2017
RadiationMonochromator: Cryo-Cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 2.708→99.524 Å / Num. obs: 24343 / % possible obs: 99.9 % / Redundancy: 56.4 % / CC1/2: 0.996 / Rpim(I) all: 0.014 / Rrim(I) all: 0.0106 / Net I/σ(I): 29.9
Reflection shellResolution: 2.71→2.81 Å / Redundancy: 39.1 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2434 / CC1/2: 0.815 / Rpim(I) all: 0.336 / Rrim(I) all: 2.17 / % possible all: 99

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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: 2.708→99.524 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.72
RfactorNum. reflection% reflection
Rfree0.2186 2433 9.99 %
Rwork0.1796 --
obs0.1824 24343 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 349.1 Å2 / Biso mean: 113.8796 Å2 / Biso min: 48.19 Å2
Refinement stepCycle: final / Resolution: 2.708→99.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2705 98 4 2807
Biso mean--71.62 69.48 -
Num. residues----126
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7082-2.76350.43091380.42131238137698
2.7635-2.82360.4131410.355112741415100
2.8236-2.88930.31361400.311712621402100
2.8893-2.96150.28911430.292912841427100
2.9615-3.04160.28261380.270412521390100
3.0416-3.13110.26551430.248512821425100
3.1311-3.23220.30451420.255112801422100
3.2322-3.34770.20971430.223512811424100
3.3477-3.48180.24231420.208212861428100
3.4818-3.64020.24871410.21312711412100
3.6402-3.83220.22451450.18413021447100
3.8322-4.07230.19511420.169112791421100
4.0723-4.38670.21221440.159212961440100
4.3867-4.82810.18811440.137712981442100
4.8281-5.52670.17991460.140113131459100
5.5267-6.96290.18751470.155413191466100
6.9629-99.59090.21931540.163113931547100
Refinement TLS params.Method: refined / Origin x: -76.678 Å / Origin y: 12.7885 Å / Origin z: -17.5249 Å
111213212223313233
T0.9073 Å2-0.2125 Å20.3328 Å2-1.9814 Å2-0.3274 Å2--2.2412 Å2
L4.9774 °20.3597 °26.5159 °2-5.7475 °2-1.0542 °2--8.9354 °2
S-0.4602 Å °-1.0266 Å °2.6389 Å °1.9982 Å °-1.9867 Å °0.8434 Å °1.6896 Å °-5.9056 Å °0.6617 Å °
Refinement TLS groupSelection details: resid 14

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