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- PDB-6up0: Structure of the Mango-III fluorescent aptamer bound to YO3-Biotin -

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Basic information

Entry
Database: PDB / ID: 6up0
TitleStructure of the Mango-III fluorescent aptamer bound to YO3-Biotin
ComponentsMango-III fluorescent aptamer
KeywordsRNA / fluorescent / aptamer
Function / homology: / YO3-biotin / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTrachman, R.J. / Ferre-D'Amare, A.R.
Citation
Journal: Rna / Year: 2021
Title: Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET.
Authors: Jeng, S.C.Y. / Trachman III, R.J. / Weissenboeck, F. / Truong, L. / Link, K.A. / Jepsen, M.D.E. / Knutson, J.R. / Andersen, E.S. / Ferre-D'Amare, A.R. / Unrau, P.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
History
DepositionOct 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Mango-III fluorescent aptamer
D: Mango-III fluorescent aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,50112
Polymers24,6472
Non-polymers85510
Water00
1
C: Mango-III fluorescent aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7516
Polymers12,3231
Non-polymers4275
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-26 kcal/mol
Surface area6150 Å2
MethodPISA
2
D: Mango-III fluorescent aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7516
Polymers12,3231
Non-polymers4275
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-25 kcal/mol
Surface area6160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.284, 66.921, 76.628
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: G / Beg label comp-ID: G / End auth comp-ID: C / End label comp-ID: C / Auth seq-ID: 1 - 38 / Label seq-ID: 1 - 38

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11chain 'C'CA
22chain 'D'DB

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Components

#1: RNA chain Mango-III fluorescent aptamer


Mass: 12323.325 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-YO3 / YO3-biotin / 3-methyl-2-[(1E,3E)-3-(1-methylquinolin-4(1H)-ylidene)prop-1-en-1-yl]-1,3-benzoxazol-3-ium


Mass: 315.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H19N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
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: 3.24 Å3/Da / Density % sol: 62.03 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 40 mM sodium cacodylate, 0.08 M sodium chloride, 0.012 M potassium chloride, 0.02 M magnesium chloride, 0.012 M spermine, 5.5% sucrose, 31% MPD
PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 24, 2018
RadiationMonochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.72→50.41 Å / Num. obs: 16604 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 89.21 Å2 / CC1/2: 0.34 / Rmerge(I) obs: 1 / Net I/σ(I): 27.6
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 1351 / CC1/2: 0.34

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Processing

Software
NameVersionClassification
PHENIX1.14_3211refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6E8S

6e8s


Resolution: 2.8→50.41 Å / SU ML: 0.5295 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3404
RfactorNum. reflection% reflection
Rfree0.2146 1498 9.87 %
Rwork0.1736 --
obs0.1777 15179 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 80.47 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1632 56 0 1688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061882
X-RAY DIFFRACTIONf_angle_d1.19752926
X-RAY DIFFRACTIONf_chiral_restr0.0514378
X-RAY DIFFRACTIONf_plane_restr0.007482
X-RAY DIFFRACTIONf_dihedral_angle_d14.2785910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.890.44431420.44311226X-RAY DIFFRACTION98.77
2.89-2.990.44941260.35711283X-RAY DIFFRACTION99.23
2.99-3.110.34891370.27441207X-RAY DIFFRACTION99.63
3.11-3.260.26461390.21841267X-RAY DIFFRACTION99.79
3.26-3.430.25261400.18361235X-RAY DIFFRACTION99.71
3.43-3.640.19321320.18971244X-RAY DIFFRACTION99.28
3.64-3.920.24861350.18641246X-RAY DIFFRACTION99.57
3.92-4.320.20061410.13891230X-RAY DIFFRACTION99.85
4.32-4.940.16551390.13251245X-RAY DIFFRACTION99.93
4.94-6.220.17921350.13241256X-RAY DIFFRACTION99.86
6.22-50.410.19141320.16751242X-RAY DIFFRACTION99.06

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