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- PDB-6bgb: Crystal Structure of the 16mer GCAGNCUUAAGUCUGC containing BrPh 7... -

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Basic information

Entry
Database: PDB / ID: 6bgb
TitleCrystal Structure of the 16mer GCAGNCUUAAGUCUGC containing BrPh 7-triazolyl-8-aza-7-deazaadenosine
Components(5'-R(*GP*CP*AP*GP*(A7C)P*CP*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3')
KeywordsRNA / duplex / structural classification / synthetic
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsFisher, A.J. / Beal, P.A. / Mumbleau, M.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM080784 United States
CitationJournal: Org. Biomol. Chem. / Year: 2017
Title: Controlling miRNA-like off-target effects of an siRNA with nucleobase modifications.
Authors: Suter, S.R. / Ball-Jones, A. / Mumbleau, M.M. / Valenzuela, R. / Ibarra-Soza, J. / Owens, H. / Fisher, A.J. / Beal, P.A.
History
DepositionOct 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 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

Downloads & links

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Assembly

Deposited unit
A: (5'-R(*GP*CP*AP*GP*(A7C)P*CP*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3')
B: (5'-R(*GP*CP*AP*GP*(A7C)P*CP*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3')
C: (5'-R(*GP*CP*AP*GP*(A7C)P*CP*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)15,9663
Polymers15,9663
Non-polymers00
Water18010
1
A: (5'-R(*GP*CP*AP*GP*(A7C)P*CP*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3')
B: (5'-R(*GP*CP*AP*GP*(A7C)P*CP*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)10,6442
Polymers10,6442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-11 kcal/mol
Surface area5980 Å2
MethodPISA
2
C: (5'-R(*GP*CP*AP*GP*(A7C)P*CP*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3')

C: (5'-R(*GP*CP*AP*GP*(A7C)P*CP*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)10,6442
Polymers10,6442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1510 Å2
ΔGint-11 kcal/mol
Surface area5980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.640, 43.150, 48.940
Angle α, β, γ (deg.)90.00, 120.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain (5'-R(*GP*CP*AP*GP*(A7C)P*CP*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3')


Mass: 5322.137 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.13 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 310.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: RNA in 10% v/v MPD, 12 mM spermine, 80 mM potassium chloride, 20 mM magnesium chloride, 40 mM sodium cacodylate, pH 7.0, equilibrated against reservoir of 35% v/v MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 19, 2016
Details: primary mirror: flat, secondary mirror: uncooled cylindrical silicon bent into toroid
RadiationMonochromator: water-cooled flat double Si(111) Khozu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 15214 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.028 / Rrim(I) all: 0.031 / Net I/σ(I): 22.5
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 3.33 / Num. unique obs: 695 / CC1/2: 0.994 / Rrim(I) all: 0.248 / % possible all: 57.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→42.187 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 48.22
RfactorNum. reflection% reflectionSelection details
Rfree0.2558 727 4.91 %Random
Rwork0.2167 ---
obs0.2188 14821 92.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→42.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1047 0 10 1057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041170
X-RAY DIFFRACTIONf_angle_d1.9671815
X-RAY DIFFRACTIONf_dihedral_angle_d7.951570
X-RAY DIFFRACTIONf_chiral_restr0.03234
X-RAY DIFFRACTIONf_plane_restr0.00754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6502-1.77760.4497780.39921967X-RAY DIFFRACTION63
1.7776-1.95650.41481420.33473004X-RAY DIFFRACTION97
1.9565-2.23960.35641500.31633027X-RAY DIFFRACTION98
2.2396-2.82150.34581890.30193024X-RAY DIFFRACTION99
2.8215-42.20050.21231680.17473072X-RAY DIFFRACTION97
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)
13.94110.0326-1.37174.89891.3916.48820.5775-0.04030.8880.37480.442-1.4308-1.2737-0.1081-0.87210.7579-0.11410.23350.6811-0.17850.64317.095116.601434.9983
25.1252-0.19651.52159.65291.67382.24360.10480.7170.35510.36771.0033-0.5607-0.74080.7713-0.9260.59410.04560.13570.44630.00230.48862.28239.07624.734
32.52871.1877-2.00790.6456-0.92191.7625-0.3539-0.08790.0047-0.81170.8910.91810.7023-0.002-0.55070.49150.0551-0.0540.70050.26950.7289-1.208320.065213.9576
46.6546-0.1165-1.35270.8376-0.32565.62150.23351.1869-0.8875-0.6539-0.41650.35530.0795-1.15680.21790.5892-0.0451-0.08770.6076-0.06130.51258.374916.24722.6738
54.32010.70092.76753.2875-0.15285.22780.8796-0.017-1.79790.27510.2979-0.21850.4941-1.0573-1.06020.7497-0.0513-0.2570.62490.07340.61333.20519.92957.1745
66.05580.4656-0.03676.23652.1617.41850.32740.7595-0.4640.88590.54370.29160.9079-0.3774-0.65030.3666-0.0226-0.07090.54250.12630.46897.322817.867617.4524
71.40740.2579-0.38773.0799-2.54622.60510.76850.04810.68841.059-0.17080.5686-0.42590.4547-0.70240.56520.10640.21330.59170.11550.7372-3.894415.349828.2427
80.9453-1.8304-0.62624.9936-0.99394.4431-0.4113-1.1340.72270.70240.4342-0.5566-1.0045-0.3905-0.05930.6102-0.0032-0.01570.5716-0.12270.53254.23038.975739.5148
90.68520.0554-0.78114.0248-3.73234.9290.3329-0.14840.8834-0.19640.84631.43480.4982-0.8319-0.93340.60840.03020.05530.85220.26710.653521.079822.145435.0122
107.36180.8092-2.16954.04170.20217.46871.13460.2137-0.1111-0.1361-0.18280.5108-0.1715-0.8809-0.88480.4947-0.0912-0.08790.4960.11370.481629.976921.747924.7354
111.8810.28442.47691.9791-0.4693.63410.25250.9455-1.07470.32060.3763-0.3215-0.15320.6319-0.7970.66810.0402-0.22670.4745-0.11880.709322.187213.24213.9471
121.918-2.02050.89015.2172-1.25024.83870.06-0.03880.0792-1.2696-0.1776-0.65010.94460.80980.10280.61170.01730.09020.678-0.01990.549720.69123.43492.6732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 4 )
2X-RAY DIFFRACTION2chain 'A' and (resid 5 through 8 )
3X-RAY DIFFRACTION3chain 'A' and (resid 9 through 12 )
4X-RAY DIFFRACTION4chain 'A' and (resid 13 through 16 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 4 )
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 8 )
7X-RAY DIFFRACTION7chain 'B' and (resid 9 through 12 )
8X-RAY DIFFRACTION8chain 'B' and (resid 13 through 16 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 4 )
10X-RAY DIFFRACTION10chain 'C' and (resid 5 through 8 )
11X-RAY DIFFRACTION11chain 'C' and (resid 9 through 12 )
12X-RAY DIFFRACTION12chain 'C' and (resid 13 through 16 )

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