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- PDB-6wtr: Structure of Human pir-miRNA-300 Apical Loop Fused to the YdaO Ri... -

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Basic information

Entry
Database: PDB / ID: 6wtr
TitleStructure of Human pir-miRNA-300 Apical Loop Fused to the YdaO Riboswitch Scaffold
ComponentsRNA (125-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 / molecular replacement / Resolution: 3.082 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: Structures of microRNA-precursor apical junctions and loops revealed by scaffold-directed crystallography: importance of non-canonical base pairs in processing
Authors: Shoffner, G.M. / Peng, Z. / Guo, F.
History
DepositionMay 3, 2020Deposition site: RCSB / Processing site: RCSB
SupersessionMay 5, 2021ID: 6N5R
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 (125-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9388
Polymers40,4131
Non-polymers1,5257
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)113.070, 113.070, 114.050
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 (125-MER)


Mass: 40412.914 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, 11 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / 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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Details

Has ligand of interestY

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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: 5.2 Å3/Da / Density % sol: 76.38 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.4
Details: 1.90 M (NH4)2SO4, 0.158 M Li2SO4, and 0.1 M NaHEPES pH 7.4

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 3.08→74.295 Å / Num. obs: 15789 / % possible obs: 99.2 % / Redundancy: 18.8 % / Biso Wilson estimate: 100.53 Å2 / CC1/2: 1 / Rpim(I) all: 0.021 / Rrim(I) all: 0.092 / Net I/σ(I): 18.9
Reflection shellResolution: 3.08→3.19 Å / Redundancy: 15.3 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1297 / CC1/2: 0.903 / Rpim(I) all: 0.344 / Rrim(I) all: 1.43 / % possible all: 92.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QK8

4qk8


Resolution: 3.082→74.295 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1922 1582 10.02 %Random selection
Rwork0.165 14207 --
obs0.1678 15789 98.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 484.75 Å2 / Biso mean: 128.3262 Å2 / Biso min: 31.82 Å2
Refinement stepCycle: final / Resolution: 3.082→74.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2676 97 4 2777
Biso mean--82.6 56.08 -
Num. residues----125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033096
X-RAY DIFFRACTIONf_angle_d0.7544823
X-RAY DIFFRACTIONf_chiral_restr0.034640
X-RAY DIFFRACTIONf_plane_restr0.003129
X-RAY DIFFRACTIONf_dihedral_angle_d18.1261541
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection Rfree: 10 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0822-3.18170.45841290.4196116891
3.1817-3.29540.30111430.27571281100
3.2954-3.42740.28221440.2205128799
3.4274-3.58330.23031420.2072127699
3.5833-3.77230.24341420.1996127999
3.7723-4.00860.23841440.1864128399
4.0086-4.31810.21911430.1636128999
4.3181-4.75250.18521460.15291306100
4.7525-5.44010.1761460.14581316100
5.4401-6.85310.15191470.14111323100
6.8531-74.2950.14931560.13531399100

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