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- PDB-6n5s: Structure of Human pir-miRNA-320b-2 Apical Loop and One-base-pair... -

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Basic information

Entry
Database: PDB / ID: 6n5s
TitleStructure of Human pir-miRNA-320b-2 Apical Loop and One-base-pair Stem Fused to the YdaO Riboswitch Scaffold
ComponentsRNA (123-MER)
KeywordsRNA / microRNA / RNA processing / Protein-RNA interaction
Function / homologyChem-2BA / GUANOSINE-5'-MONOPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.802 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
Revision 2.0Oct 16, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (123-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,86411
Polymers39,9281
Non-polymers1,93710
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.560, 114.560, 115.060
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 (123-MER)


Mass: 39927.621 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 , 6 types, 16 molecules

#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: 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
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 5.46 Å3/Da / Density % sol: 77.47 %
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: 2.8→75.137 Å / Num. obs: 21893 / % possible obs: 99.9 % / Redundancy: 9.92 % / CC1/2: 0.998 / Rpim(I) all: 0.02 / Rrim(I) all: 0.062 / Net I/σ(I): 23
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 9.95 % / CC1/2: 0.709 / Rpim(I) all: 0.499 / Rrim(I) all: 1.73 / % possible all: 99.7

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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: 2.802→75.137 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.04
RfactorNum. reflection% reflectionSelection details
Rfree0.2008 2184 10.01 %Random selection
Rwork0.1765 ---
obs0.1789 21828 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 457.69 Å2 / Biso mean: 122.0111 Å2 / Biso min: 47.01 Å2
Refinement stepCycle: final / Resolution: 2.802→75.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2640 122 6 2768
Biso mean--89.34 78.86 -
Num. residues----123
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 (%)
2.8025-2.86340.41651340.46451204133899
2.8634-2.930.36971330.376811991332100
2.93-3.00330.39081350.343312141349100
3.0033-3.08450.31091350.273412091344100
3.0845-3.17530.27091350.254712171352100
3.1753-3.27770.30081350.253412131348100
3.2777-3.39490.24931330.228912041337100
3.3949-3.53080.23541370.210612311368100
3.5308-3.69150.21911360.207912211357100
3.6915-3.88610.19431340.182312061340100
3.8861-4.12960.21421360.172812281364100
4.1296-4.44840.17581370.15112241361100
4.4484-4.8960.15461380.146412421380100
4.896-5.60420.15661390.135712571396100
5.6042-7.05990.15721400.147912571397100
7.0599-75.16390.20271470.157813181465100
Refinement TLS params.Method: refined / Origin x: -78.0159 Å / Origin y: 18.698 Å / Origin z: -13.9445 Å
111213212223313233
T1.5093 Å20.678 Å20.3333 Å2-2.9648 Å2-1.0105 Å2--3.8091 Å2
L0.8484 °22.3753 °2-2.15 °2-5.5632 °2-5.4182 °2--5.4475 °2
S-1.9332 Å °-2.6433 Å °4.5095 Å °0.2047 Å °1.2322 Å °4.1862 Å °-2.3619 Å °-4.4511 Å °1.1681 Å °
Refinement TLS groupSelection details: resid 14:19

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