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

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Basic information

Entry
Database: PDB / ID: 6jjh
TitleCrystal structure of a two-quartet RNA parallel G-quadruplex complexed with the porphyrin TMPyP4
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 / SAD / Resolution: 1.74 Å
AuthorsZhang, Y.S. / EI Omari, K. / Duman, R. / Wagner, A. / Parkinson, G.N. / Wei, D.G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31672558 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: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / 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 / _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 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)6,0486
Polymers4,5731
Non-polymers1,4755
Water19811
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)12,09512
Polymers9,1462
Non-polymers2,95010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area5530 Å2
ΔGint-42 kcal/mol
Surface area3690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.856, 23.647, 31.052
Angle α, β, γ (deg.)90.000, 107.590, 90.000
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11B-104-

K

21B-105-

K

31B-202-

HOH

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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-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.: 2 / Source method: obtained synthetically / Formula: C44H38N8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.17 % / Description: rod like crystals
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

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I2311.7712
SYNCHROTRONDiamond I2323.3509
Detector
TypeIDDetectorDate
DECTRIS PILATUS 12M1PIXELJun 27, 2018
DECTRIS PILATUS 12M2PIXELJun 27, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.77121
23.35091
Reflection

Entry-ID: 6JJH

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.74-29.6437799.56.2410.021115.6
2.19-29.6206592.17.80.9860.116213.9
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.74-1.80.341.764310.842198.6
2.19-2.310.3383.82540.9152

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
Aimlessdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 1.74→29.6 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.911 / SU B: 4.661 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2914 236 5.4 %RANDOM
Rwork0.2393 ---
obs0.2418 4142 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.63 Å2 / Biso mean: 42.481 Å2 / Biso min: 21.04 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å20 Å20.38 Å2
2---1.47 Å2-0 Å2
3---2.24 Å2
Refinement stepCycle: final / Resolution: 1.74→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 303 107 11 421
Biso mean--44.3 41.21 -
Num. residues----14
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.013459
X-RAY DIFFRACTIONr_bond_other_d0.0020.019216
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.335705
X-RAY DIFFRACTIONr_angle_other_deg1.3792.547488
X-RAY DIFFRACTIONr_chiral_restr0.1050.256
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02454
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02133
LS refinement shellResolution: 1.74→1.785 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 16 -
Rwork0.365 290 -
all-306 -
obs--97.76 %

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