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- PDB-6zpf: Racemic compound of RNA duplexes. -

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Basic information

Entry
Database: PDB / ID: 6zpf
TitleRacemic compound of RNA duplexes.
Components
  • RNA (5'-R(*(0C)P*(0C)P*(0G)P*(0C)P*(0C)P*(0U)P*(0G)P*(0G))-3')
  • RNA (5'-R(*(0C)P*(0U)P*(0G)P*(0G)P*(0G)P*(0C)P*(0G)P*(0G))-3')
  • RNA (5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3')
  • RNA (5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3')
KeywordsRNA / racemic compound
Function / homologyRNA
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.442 Å
AuthorsRypniewski, W.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Broken symmetry between RNA enantiomers in a crystal lattice.
Authors: Kiliszek, A. / Blaszczyk, L. / Bejger, M. / Rypniewski, W.
History
DepositionJul 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Jul 26, 2023Group: Derived calculations / Polymer sequence / Category: atom_type / entity_poly
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _entity_poly.type
Revision 2.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
K: RNA (5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3')
L: RNA (5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3')
M: RNA (5'-R(*(0C)P*(0U)P*(0G)P*(0G)P*(0G)P*(0C)P*(0G)P*(0G))-3')
N: RNA (5'-R(*(0C)P*(0C)P*(0G)P*(0C)P*(0C)P*(0U)P*(0G)P*(0G))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,68811
Polymers10,2304
Non-polymers4587
Water3,549197
1
K: RNA (5'-R(*CP*UP*GP*GP*GP*CP*GP*G)-3')
L: RNA (5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3776
Polymers5,1152
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
M: RNA (5'-R(*(0C)P*(0U)P*(0G)P*(0G)P*(0G)P*(0C)P*(0G)P*(0G))-3')
N: RNA (5'-R(*(0C)P*(0C)P*(0G)P*(0C)P*(0C)P*(0U)P*(0G)P*(0G))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3115
Polymers5,1152
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)20.850, 26.500, 38.570
Angle α, β, γ (deg.)106.107, 96.001, 92.722
Int Tables number1
Space group name H-MP1

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Components

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RNA chain , 4 types, 4 molecules KLMN

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


Mass: 2597.601 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chain K is D-enantiomer. It pairs with chain L. / Source: (synth.) Thermus thermophilus (bacteria)
#2: RNA chain RNA (5'-R(*CP*CP*GP*CP*CP*UP*GP*G)-3')


Mass: 2517.553 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chain L is D-enantiomer. It pairs with chain K. / Source: (synth.) Thermus thermophilus (bacteria)
#3: RNA chain RNA (5'-R(*(0C)P*(0U)P*(0G)P*(0G)P*(0G)P*(0C)P*(0G)P*(0G))-3')


Mass: 2597.601 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chain M is L-enantiomer. It pairs with chain N. / Source: (synth.) Thermus thermophilus (bacteria)
#4: RNA chain RNA (5'-R(*(0C)P*(0C)P*(0G)P*(0C)P*(0C)P*(0U)P*(0G)P*(0G))-3')


Mass: 2517.553 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria)

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Non-polymers , 2 types, 204 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.98 Å3/Da / Density % sol: 38 % / Description: needle
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M zinc acetate, 0.1 M cacodylate buffer, 18% w/v polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.283 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 1.44→40 Å / Num. obs: 12417 / % possible obs: 87.3 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.061 / Net I/σ(I): 11.04
Reflection shellResolution: 1.44→1.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 2.49 / Num. unique obs: 5931 / CC1/2: 0.963 / Rrim(I) all: 0.343 / % possible all: 74.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZQ9

6zq9


Resolution: 1.442→36.776 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.94 / SU ML: 0.073 / Cross valid method: FREE R-VALUE / ESU R: 0.101 / ESU R Free: 0.105
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2497 653 5.262 %
Rwork0.2011 11757 -
all0.204 --
obs-12410 87.505 %
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: 17.245 Å2
Baniso -1Baniso -2Baniso -3
1--0.832 Å20.206 Å2-0.676 Å2
2--1.894 Å20.141 Å2
3----0.838 Å2
Refinement stepCycle: LAST / Resolution: 1.442→36.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 676 7 197 880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.011752
X-RAY DIFFRACTIONr_bond_other_d0.0030.019292
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.4521168
X-RAY DIFFRACTIONr_angle_other_deg1.2062.383726
X-RAY DIFFRACTIONr_chiral_restr0.0610.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.02412
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02124
X-RAY DIFFRACTIONr_nbd_refined0.2160.2101
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2670.2394
X-RAY DIFFRACTIONr_nbtor_refined0.2470.2272
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0590.2152
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2620.2172
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.250.22
X-RAY DIFFRACTIONr_metal_ion_refined0.2340.213
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1460.212
X-RAY DIFFRACTIONr_nbd_other0.170.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1960.228
X-RAY DIFFRACTIONr_scbond_it1.3251.644752
X-RAY DIFFRACTIONr_scbond_other1.3251.644750
X-RAY DIFFRACTIONr_scangle_it1.6932.4761168
X-RAY DIFFRACTIONr_scangle_other1.6932.4761169
X-RAY DIFFRACTIONr_lrange_it4.96118.571151
X-RAY DIFFRACTIONr_lrange_other4.1617.1821065
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.442-1.4790.269430.2995940.29710620.8020.78459.98120.268
1.479-1.520.374600.2688190.2759930.7680.83588.51960.24
1.52-1.5640.314510.2488310.25210170.8480.85786.72570.226
1.564-1.6120.278420.268000.269640.8590.87587.34440.238
1.612-1.6650.257390.2327570.2349170.9040.89486.80480.21
1.665-1.7230.257380.2127990.2149200.9260.92290.97830.194
1.723-1.7880.241400.2037090.2058550.9030.92487.60230.187
1.788-1.8610.274250.2217390.2238520.90.90889.67140.203
1.861-1.9430.262390.236850.2328090.9040.90189.49320.219
1.943-2.0380.311380.2236640.2287760.860.90990.46390.219
2.038-2.1470.31250.2096420.2137270.8930.93591.74690.217
2.147-2.2770.299280.2085790.2126790.9150.93389.39620.218
2.277-2.4340.224310.2045560.2056550.9310.93489.61830.221
2.434-2.6280.351240.1995590.2056220.9240.93793.72990.226
2.628-2.8770.248360.2114720.2145550.9250.93991.53150.247
2.877-3.2140.303290.1944140.2014950.8930.95289.49490.242
3.214-3.7070.144160.1684030.1674460.9790.96993.94620.232
3.707-4.5290.17210.1433310.1453740.970.96694.11760.226
4.529-6.3560.22180.1462490.1522970.9450.96389.8990.229
6.356-36.7760.187100.1951540.1941660.9640.94998.79520.292

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