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- PDB-6wtl: Structure of Human pir-miRNA-19b-2 Apical Loop and One-base-pair ... -

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Basic information

Entry
Database: PDB / ID: 6wtl
TitleStructure of Human pir-miRNA-19b-2 Apical Loop and One-base-pair Fused to the YdaO Riboswitch Scaffold
ComponentsRNA (124-MER)
KeywordsRNA / microRNA / RNA processing
Function / homologyChem-2BA / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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
DepositionMay 3, 2020Deposition site: RCSB / Processing site: RCSB
SupersessionMay 5, 2021ID: 6N5L
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 (124-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7999
Polymers40,2501
Non-polymers1,5498
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.340, 115.340, 115.280
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 (124-MER)


Mass: 40249.789 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, 9 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.: 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.: 1 / 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

Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 1.7 M (NH4)2SO4, 0.2 M LI2SO4, AND 0.1 M HEPES PH 7.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.85→75.491 Å / Num. obs: 21107 / % possible obs: 100 % / Redundancy: 19.8 % / Biso Wilson estimate: 97.99 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.014 / Rrim(I) all: 0.061 / Net I/σ(I): 32.8
Reflection shellResolution: 2.85→2.92 Å / Redundancy: 17.9 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1386 / CC1/2: 0.816 / Rpim(I) all: 0.358 / Rrim(I) all: 1.62 / % possible all: 99.8

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Processing

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

4qk8


Resolution: 2.85→75.491 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 2110 10 %Random selection
Rwork0.1873 18997 --
obs0.1898 21107 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 386.84 Å2 / Biso mean: 118.379 Å2 / Biso min: 47.85 Å2
Refinement stepCycle: final / Resolution: 2.85→75.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2661 98 1 2760
Biso mean--70.91 47.85 -
Num. residues----124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033081
X-RAY DIFFRACTIONf_angle_d0.7664801
X-RAY DIFFRACTIONf_chiral_restr0.036635
X-RAY DIFFRACTIONf_plane_restr0.004128
X-RAY DIFFRACTIONf_dihedral_angle_d17.1931529
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 (%)
2.8502-2.91650.53581390.44651247100
2.9165-2.98940.43791390.39121257100
2.9894-3.07030.34171350.30381220100
3.0703-3.16060.27471400.24241254100
3.1606-3.26260.29211420.23351278100
3.2626-3.37920.24341380.22921240100
3.3792-3.51450.24991370.22011236100
3.5145-3.67450.2071410.21181277100
3.6745-3.86820.22191400.18321258100
3.8682-4.11060.2011390.17721247100
4.1106-4.42790.17681410.16191269100
4.4279-4.87340.16511410.14961276100
4.8734-5.57840.16481420.14391272100
5.5784-7.02740.19651440.1611302100
7.0274-75.490.22071520.1917136499

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