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- PDB-6xrq: Structural descriptions of ligand interactions to DNA and RNA qua... -

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Basic information

Entry
Database: PDB / ID: 6xrq
TitleStructural descriptions of ligand interactions to DNA and RNA quadruplexes folded from the non-coding region of Pseudorabies virus
ComponentsRNA (5' GP*GP*CP*UP*CP*GP*GP*CP*GP*GP*CP*GP*GP*A-3')
KeywordsRNA / Quadruplex / PRV
Function / homology: / Chem-V8A / RNA / RNA (> 10)
Function and homology information
Biological speciesPseudorabies virus Ea
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.21 Å
AuthorsZhang, Y.S. / Parkinson, G.N. / Wei, D.G.
CitationJournal: Biochimie / Year: 2024
Title: Structural descriptions of ligand interactions to RNA quadruplexes folded from the non-coding region of Pseudorabies virus.
Authors: Zhang, Y. / Bux, K. / Attana, F. / Wei, D. / Haider, S. / Parkinson, G.N.
History
DepositionJul 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 26, 2024Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)10,8737
Polymers9,1462
Non-polymers1,7275
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-23 kcal/mol
Surface area5630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.177, 43.974, 30.781
Angle α, β, γ (deg.)90.000, 108.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 4572.788 Da / Num. of mol.: 2 / 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
#3: Chemical ChemComp-V8A / 2,7-bis[3-(morpholin-4-yl)propyl]-4,9-bis{[3-(morpholin-4-yl)propyl]amino}benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone


Mass: 804.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H60N8O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Absorpt correction T max: 1 / Absorpt correction T min: 0.949905760669 / Absorpt correction type: empirical
Absorpt process details: CCP4 7.0.075: AIMLESS, version 0.7.4 : 13/12/18 Scaling & analysis of unmerged intensities, absorption correction using spherical harmonics
Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.97 % / Mosaicity: 0 °
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Potassium cacodylate, Potassium chloride, Sodium cacodylate, MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96864 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 29, 2019
RadiationMonochromator: si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96864 Å / Relative weight: 1
ReflectionLimit h max: 20 / Limit h min: -21 / Limit k max: 28 / Limit k min: -29 / Limit l max: 23 / Limit l min: -21 / Number: 47094 / Theta max: 23.6140252043 ° / Theta min: 0.934183571367 °
ReflectionResolution: 1.21→27.703 Å / Num. obs: 21248 / % possible obs: 94.1 % / Redundancy: 5.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.028 / Rrim(I) all: 0.072 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.21-1.233.10.5996280.8530.3870.71856.5
6.63-27.7036.20.0731510.9890.0320.0899.3
Cell measurementReflection used: 47094 / Theta max: 23.6140252043 ° / Theta min: 0.934183571367 °

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JJH

6jjh


Resolution: 1.21→27.69 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 0.926 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.056 / ESU R Free: 0.056
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1025 4.829 %Random Selection
Rwork0.199 20202 --
all0.2 ---
obs0.1999 21227 93.879 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.412 Å2-0 Å2-0.107 Å2
2--1.5 Å2-0 Å2
3----0.833 Å2
Refinement stepCycle: final / Resolution: 1.21→27.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 606 119 97 822
Biso mean--18.26 27.65 -
Num. residues----28
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.012853
X-RAY DIFFRACTIONr_bond_other_d0.0040.02290
X-RAY DIFFRACTIONr_angle_refined_deg2.0011.4891283
X-RAY DIFFRACTIONr_angle_other_deg1.823696
X-RAY DIFFRACTIONr_chiral_restr0.120.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0320.02418
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02168
X-RAY DIFFRACTIONr_nbd_refined0.2370.2138
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2280.2342
X-RAY DIFFRACTIONr_nbtor_refined0.2740.2319
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0630.2142
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.267
X-RAY DIFFRACTIONr_metal_ion_refined0.0630.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1290.232
X-RAY DIFFRACTIONr_nbd_other0.2030.223
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0680.28
X-RAY DIFFRACTIONr_scbond_it1.9171.747853
X-RAY DIFFRACTIONr_scbond_other1.8321.738724
X-RAY DIFFRACTIONr_scangle_it2.9432.6331283
X-RAY DIFFRACTIONr_scangle_other2.8282.6471104
X-RAY DIFFRACTIONr_lrange_it4.126.1793561
X-RAY DIFFRACTIONr_lrange_other3.94727.3862942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.2410.319560.337917X-RAY DIFFRACTION58.5792
1.241-1.2750.372490.3021127X-RAY DIFFRACTION72.5478
1.275-1.3120.329660.2851309X-RAY DIFFRACTION87.6354
1.312-1.3530.287690.2681420X-RAY DIFFRACTION96.4378
1.353-1.3970.31710.2351404X-RAY DIFFRACTION100
1.397-1.4460.308490.2351375X-RAY DIFFRACTION100
1.446-1.50.224500.2341315X-RAY DIFFRACTION100
1.5-1.5610.259480.2051318X-RAY DIFFRACTION99.9268
1.561-1.6310.179660.1821224X-RAY DIFFRACTION100
1.631-1.710.175630.1761157X-RAY DIFFRACTION100
1.71-1.8020.215610.1721097X-RAY DIFFRACTION100
1.802-1.9110.205640.1931039X-RAY DIFFRACTION100
1.911-2.0420.223560.188995X-RAY DIFFRACTION100
2.042-2.2050.191470.187925X-RAY DIFFRACTION100
2.205-2.4140.178500.204831X-RAY DIFFRACTION100
2.414-2.6970.232620.193759X-RAY DIFFRACTION100
2.697-3.1090.192420.202677X-RAY DIFFRACTION100
3.109-3.7970.208360.168574X-RAY DIFFRACTION100
3.797-5.3250.2160.164457X-RAY DIFFRACTION100
5.325-27.690.39240.255282X-RAY DIFFRACTION100

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