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- PDB-3nj6: 0.95 A resolution X-ray structure of (GGCAGCAGCC)2 -

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Basic information

Entry
Database: PDB / ID: 3nj6
Title0.95 A resolution X-ray structure of (GGCAGCAGCC)2
Components5'-R(*GP*GP*CP*AP*GP*CP*AP*GP*CP*C)-3'
KeywordsRNA / CAG repeats / polyQ diseases
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsKiliszek, A. / Kierzek, R. / Krzyzosiak, W.J. / Rypniewski, W.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Atomic resolution structure of CAG RNA repeats: structural insights and implications for the trinucleotide repeat expansion diseases.
Authors: Kiliszek, A. / Kierzek, R. / Krzyzosiak, W.J. / Rypniewski, W.
History
DepositionJun 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*GP*GP*CP*AP*GP*CP*AP*GP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,3112
Polymers3,2151
Non-polymers961
Water1,36976
1
A: 5'-R(*GP*GP*CP*AP*GP*CP*AP*GP*CP*C)-3'
hetero molecules

A: 5'-R(*GP*GP*CP*AP*GP*CP*AP*GP*CP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6224
Polymers6,4302
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area970 Å2
ΔGint-4 kcal/mol
Surface area3900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.427, 46.427, 82.678
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-12-

HOH

21A-18-

HOH

31A-25-

HOH

41A-39-

HOH

51A-56-

HOH

61A-62-

HOH

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Components

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


Mass: 3215.004 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 292 K / pH: 8.5
Details: MgSO4, (NH4)2SO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.8
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 6, 2009
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.95→23.213 Å / Num. obs: 21756 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 15.3 % / Biso Wilson estimate: 6.8 Å2 / Rsym value: 0.036 / Net I/σ(I): 74.1
Reflection shellResolution: 0.95→0.97 Å / Redundancy: 11 % / Mean I/σ(I) obs: 7.7 / Rsym value: 0.291 / % possible all: 98

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Phasing

Phasing MRRfactor: 61.16 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å23.21 Å
Translation2.5 Å23.21 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.1phasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A-RNA HELIX

Resolution: 0.95→23.21 Å / Occupancy max: 1 / Occupancy min: 0.15 / SU ML: 0.08 / Isotropic thermal model: anisotropic / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rwork0.106 --
obs0.106 21748 99.7 %
Rfree-0 100 %
all-21748 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.58 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso mean: 11.44 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati sigma a obs: 0.08 Å
Refinement stepCycle: LAST / Resolution: 0.95→23.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 213 5 76 294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016242
X-RAY DIFFRACTIONf_angle_d1.996376
X-RAY DIFFRACTIONf_dihedral_angle_d14.30296
X-RAY DIFFRACTIONf_chiral_restr0.09849
X-RAY DIFFRACTIONf_plane_restr0.03110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.952-0.9630.1116990.111699X-RAY DIFFRACTION94
0.963-0.9740.1016900.101690X-RAY DIFFRACTION99
0.974-0.9860.0947440.094744X-RAY DIFFRACTION100
0.986-0.9980.0876870.087687X-RAY DIFFRACTION100
0.998-1.0120.0827250.082725X-RAY DIFFRACTION100
1.012-1.0250.0727090.072709X-RAY DIFFRACTION100
1.025-1.040.0757330.075733X-RAY DIFFRACTION100
1.04-1.0560.0747190.074719X-RAY DIFFRACTION100
1.056-1.0720.0687180.068718X-RAY DIFFRACTION100
1.072-1.090.0627040.062704X-RAY DIFFRACTION100
1.09-1.1090.0657130.065713X-RAY DIFFRACTION100
1.109-1.1290.0667270.066727X-RAY DIFFRACTION100
1.129-1.150.0647110.064711X-RAY DIFFRACTION100
1.15-1.1740.0597180.059718X-RAY DIFFRACTION100
1.174-1.1990.0667370.066737X-RAY DIFFRACTION100
1.199-1.2270.0667270.066727X-RAY DIFFRACTION100
1.227-1.2580.0717050.071705X-RAY DIFFRACTION100
1.258-1.2920.0677310.067731X-RAY DIFFRACTION100
1.292-1.330.0717230.071723X-RAY DIFFRACTION100
1.33-1.3730.0737280.073728X-RAY DIFFRACTION100
1.373-1.4220.087240.08724X-RAY DIFFRACTION100
1.422-1.4790.0817320.081732X-RAY DIFFRACTION100
1.479-1.5460.0917320.091732X-RAY DIFFRACTION100
1.546-1.6280.0917160.091716X-RAY DIFFRACTION100
1.628-1.730.0917390.091739X-RAY DIFFRACTION100
1.73-1.8630.1027240.102724X-RAY DIFFRACTION100
1.863-2.050.1217420.121742X-RAY DIFFRACTION100
2.05-2.3470.1267400.126740X-RAY DIFFRACTION100
2.347-2.9560.1417590.141759X-RAY DIFFRACTION100
2.956-23.220.1497920.149792X-RAY DIFFRACTION99

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