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- PDB-6q8v: Structure of the standard kink turn HmKt-7 variant A2bm6A. -

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Basic information

Entry
Database: PDB / ID: 6q8v
TitleStructure of the standard kink turn HmKt-7 variant A2bm6A.
ComponentsRNA (5'-R(*GP*GP*CP*GP*AP*AP*GP*(6MZ)P*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')
KeywordsRNA / Gene regulation / RNA structure / kink-turn / X-ray crystallography / RNA modification
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHaloarcula marismortui (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsHuang, L. / Lilley, D.M.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKA18604 United Kingdom
CitationJournal: Rna Biol. / Year: 2019
Title: Effect of methylation of adenine N6on kink turn structure depends on location.
Authors: Ashraf, S. / Huang, L. / Lilley, D.M.J.
History
DepositionDec 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 11, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*GP*GP*CP*GP*AP*AP*GP*(6MZ)P*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,2481
Polymers6,2481
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint5 kcal/mol
Surface area3440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.660, 70.660, 48.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: RNA chain RNA (5'-R(*GP*GP*CP*GP*AP*AP*GP*(6MZ)P*AP*CP*CP*GP*GP*GP*GP*AP*GP*CP*C)-3')


Mass: 6247.860 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Haloarcula marismortui (Halophile)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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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: 2.8 Å3/Da / Density % sol: 56.05 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Potassium chloride, 0.002 M Spermine tetrahydrochloride, 0.05 M Bis-Tris 7.0, 15 % w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9197 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9197 Å / Relative weight: 1
ReflectionResolution: 2.09→35.33 Å / Num. obs: 4521 / % possible obs: 99 % / Observed criterion σ(I): 1.4 / Redundancy: 12.1 % / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.011 / Net I/σ(I): 29.7
Reflection shellResolution: 2.09→2.13 Å / Redundancy: 12.2 % / Rmerge(I) obs: 2.28 / Num. unique obs: 218 / CC1/2: 0.67 / Rpim(I) all: 0.67 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4cs1

4cs1


Resolution: 2.09→35.33 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.03
RfactorNum. reflection% reflection
Rfree0.2107 214 4.74 %
Rwork0.2054 --
obs0.2057 4511 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.09→35.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 415 0 1 416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005465
X-RAY DIFFRACTIONf_angle_d1.004723
X-RAY DIFFRACTIONf_dihedral_angle_d13.244213
X-RAY DIFFRACTIONf_chiral_restr0.0493
X-RAY DIFFRACTIONf_plane_restr0.00719
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0902-2.63330.38471090.33932080X-RAY DIFFRACTION99
2.6333-35.3350.19031050.19122217X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.09160.2485-0.07420.895-0.24480.2880.27430.6749-0.29410.05390.112-0.74141.02770.2741-0.00060.9788-0-0.04410.638-0.28970.8623232.504968.3954152.4793
22.62172.2042-1.33872.8347-2.38893.19190.5580.47980.2261-0.20390.13990.63090.3883-1.18460.00110.9988-0.0285-0.00750.6296-0.02120.7434227.442179.8995148.8575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 5 )
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 19 )

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