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- PDB-6pq7: Structure of the iMango-III fluorescent aptamer at room temperature. -

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Basic information

Entry
Database: PDB / ID: 6pq7
TitleStructure of the iMango-III fluorescent aptamer at room temperature.
ComponentsRNA (37-MER)
KeywordsRNA / fluorescent / aptamer / XFELS
Function / homology: / Chem-OXV / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsTrachman III, R.J. / Ferre-D'Amare, A.R.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Co-crystal structure of the iMango-III fluorescent RNA aptamer using an X-ray free-electron laser.
Authors: Trachman III, R.J. / Stagno, J.R. / Conrad, C. / Jones, C.P. / Fischer, P. / Meents, A. / Wang, Y.X. / Ferre-D'Amare, A.R.
#1: 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
DepositionJul 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2019Group: Data collection / 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 1.2Aug 28, 2019Group: Data collection / Database references / Category: citation_author / reflns / reflns_shell
Item: _citation_author.name / _reflns.pdbx_R_split / _reflns_shell.pdbx_R_split
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: RNA (37-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7224
Polymers12,0501
Non-polymers6723
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.560, 53.560, 194.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11C-101-

MG

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Components

#1: RNA chain RNA (37-MER)


Mass: 12050.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-OXV / ~{N}-[2-[2-[2-[2-[2-[2-[(1-methylquinolin-4-yl)methyl]-1,3-benzothiazol-3-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethyl]pentanamide


Mass: 608.791 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H44N4O5S
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
Has ligand of interestN

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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: 2.9 Å3/Da / Density % sol: 57.56 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 0.1 M Na cacodylate pH 7.1, 17.5% (w/v) polyethylene glycol (PEG) 3350, and 0.25 M Magnesium acetate

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Data collection

DiffractionMean temperature: 296 K / Ambient temp details: room temperature / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.303 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.303 Å / Relative weight: 1
ReflectionResolution: 3→52.5 Å / Num. obs: 5419 / % possible obs: 99.9 % / Redundancy: 3 % / Biso Wilson estimate: 56.8 Å2 / CC1/2: 0.7 / R split: 0.53 / Net I/σ(I): 2.3
Reflection shellResolution: 3→3.3 Å / Redundancy: 3 % / Num. unique obs: 368 / CC1/2: 0.245 / R split: 1.421 / % possible all: 100
Serial crystallography measurementFocal spot size: 1 µm2 / Pulse duration: 0.044 fsec.
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E8U

6e8u


Resolution: 3→51.64 Å / SU ML: 0.3945 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.2294
RfactorNum. reflection% reflection
Rfree0.3044 538 9.93 %
Rwork0.2688 --
obs0.2726 5419 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.19 Å2
Refinement stepCycle: LAST / Resolution: 3→51.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 796 45 0 841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056938
X-RAY DIFFRACTIONf_angle_d1.14121451
X-RAY DIFFRACTIONf_chiral_restr0.0473183
X-RAY DIFFRACTIONf_plane_restr0.006241
X-RAY DIFFRACTIONf_dihedral_angle_d17.7288454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.30.31951320.26141212X-RAY DIFFRACTION99.93
3.3-3.780.27381310.25271218X-RAY DIFFRACTION99.78
3.78-4.760.28591380.26121228X-RAY DIFFRACTION100
4.76-51.640.33141370.2871223X-RAY DIFFRACTION99.85

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