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- PDB-6jji: Crystal structure of a two-quartet RNA parallel G-quadruplex comp... -

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Basic information

Entry
Database: PDB / ID: 6jji
TitleCrystal structure of a two-quartet RNA parallel G-quadruplex complexed with the porphyrin TMPyP4 (1:1)
ComponentsRNA (5'-R(*GP*GP*CP*UP*CP*GP*GP*CP*GP*GP*CP*GP*GP*A)-3')
KeywordsRNA / G-quadruplex / two-quartet / complex
Function / homology: / Chem-POH / RNA / RNA (> 10)
Function and homology information
Biological speciesPseudorabies virus Ea
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsZhang, Y.S. / Parkinson, G.N. / Wei, D.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31672558 China
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Native de novo structural determinations of non-canonical nucleic acid motifs by X-ray crystallography at long wavelengths.
Authors: Zhang, Y. / El Omari, K. / Duman, R. / Liu, S. / Haider, S. / Wagner, A. / Parkinson, G.N. / Wei, D.
History
DepositionFeb 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / refine_ls_shell / reflns_shell / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine_ls_shell.d_res_low / _reflns_shell.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry
Revision 1.2Oct 7, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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:
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Assembly

Deposited unit
B: RNA (5'-R(*GP*GP*CP*UP*CP*GP*GP*CP*GP*GP*CP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3695
Polymers4,5731
Non-polymers7964
Water00
1
B: RNA (5'-R(*GP*GP*CP*UP*CP*GP*GP*CP*GP*GP*CP*GP*GP*A)-3')
hetero molecules

B: RNA (5'-R(*GP*GP*CP*UP*CP*GP*GP*CP*GP*GP*CP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,73810
Polymers9,1462
Non-polymers1,5928
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area900 Å2
ΔGint-4 kcal/mol
Surface area5440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.509, 29.244, 57.557
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11B-101-

K

21B-102-

K

31B-103-

K

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Components

#1: RNA chain RNA (5'-R(*GP*GP*CP*UP*CP*GP*GP*CP*GP*GP*CP*GP*GP*A)-3')


Mass: 4572.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pseudorabies virus Ea
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-POH / (1Z,4Z,9Z,15Z)-5,10,15,20-tetrakis(1-methylpyridin-1-ium-4-yl)-21,23-dihydroporphyrin / TMPyP4


Mass: 678.826 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H38N8 / Feature type: SUBJECT OF INVESTIGATION
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: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Potassium cacodylate, Sodium cacodylate, Potassium chloride, MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→16.042 Å / Num. obs: 825 / % possible obs: 96.57 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 8.6
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.403 / Num. unique obs: 79

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JJH

6jjh


Resolution: 3.1→16.042 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 2.17 / Phase error: 16.95 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflection
Rfree0.2497 36 4.41 %
Rwork0.1927 781 -
obs0.195 817 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.81 Å2 / Biso mean: 71.0763 Å2 / Biso min: 34.62 Å2
Refinement stepCycle: final / Resolution: 3.1→16.042 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 303 55 0 358
Biso mean--70.59 --
Num. residues----14
LS refinement shellResolution: 3.1→3.21 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2497 36 -
Rwork0.1927 781 -
obs--97 %
Refinement TLS params.Method: refined / Origin x: 8.0762 Å / Origin y: 2.9584 Å / Origin z: 4.4843 Å
111213212223313233
T0.4487 Å20.1394 Å20.0071 Å2-0.5065 Å20.085 Å2--0.5806 Å2
L3.742 °20.3343 °20.0303 °2-9.3281 °2-0.9756 °2--2.832 °2
S0.1476 Å °-0.0432 Å °0.3778 Å °1.56 Å °-0.2791 Å °0.2917 Å °-0.3647 Å °-0.1161 Å °0.2184 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB1 - 14
2X-RAY DIFFRACTION1allC1 - 3
3X-RAY DIFFRACTION1allT1

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