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- PDB-3nj7: 1.9 A resolution X-ray structure of (GGCAGCAGCC)2 -

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Basic information

Entry
Database: PDB / ID: 3nj7
Title1.9 A resolution X-ray structure of (GGCAGCAGCC)2
Components5'-R(*GP*GP*CP*AP*GP*CP*AP*GP*CP*C)-3'
KeywordsRNA / CAG repeats / poly-Q diseases
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.904 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 / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)19,86612
Polymers19,2906
Non-polymers5766
Water3,189177
1
A: 5'-R(*GP*GP*CP*AP*GP*CP*AP*GP*CP*C)-3'
B: 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
Buried area990 Å2
ΔGint-3 kcal/mol
Surface area3930 Å2
MethodPISA
2
C: 5'-R(*GP*GP*CP*AP*GP*CP*AP*GP*CP*C)-3'
D: 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
Buried area980 Å2
ΔGint-4 kcal/mol
Surface area3930 Å2
MethodPISA
3
E: 5'-R(*GP*GP*CP*AP*GP*CP*AP*GP*CP*C)-3'
F: 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
Buried area990 Å2
ΔGint-4 kcal/mol
Surface area3920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.366, 47.366, 83.209
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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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.: 6 / Source method: obtained synthetically
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.79 Å3/Da / Density % sol: 55.97 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: MgSO4, (NH4)2SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 28, 2009
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.9→18.6 Å / Num. all: 16346 / Num. obs: 16346 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 25.7 Å2 / Rsym value: 0.105 / Net I/σ(I): 18.2
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 801 / Rsym value: 0.518 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NJ6

3nj6


Resolution: 1.904→18.553 Å / SU ML: 0.21 / Isotropic thermal model: TLS refinement / Cross valid method: THROUGHOUT / σ(F): 1.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2482 821 5.06 %RANDOM
Rwork0.2117 ---
all0.2136 16234 --
obs0.2136 16234 99.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.154 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso mean: 24.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.9073 Å2-0 Å20 Å2
2---0.9073 Å2-0 Å2
3---1.8146 Å2
Refine analyzeLuzzati sigma a obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.904→18.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1278 30 177 1485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061452
X-RAY DIFFRACTIONf_angle_d1.3722256
X-RAY DIFFRACTIONf_dihedral_angle_d13.419576
X-RAY DIFFRACTIONf_chiral_restr0.054294
X-RAY DIFFRACTIONf_plane_restr0.00560
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.904-2.02290.30831350.251725802715100
2.0229-2.17880.22851230.214725932716100
2.1788-2.39770.22381510.195325622713100
2.3977-2.74370.24171420.207825892731100
2.7437-3.45310.23831410.20652552269399
3.4531-18.55380.25751290.20792537266698
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)
10.8218-0.4262.47971.5973-3.84183.21570.13950.02080.0101-0.2612-0.0108-0.02990.25490.185-0.12890.32650.0940.01480.1995-0.02840.122619.9554-15.23864.6906
20.19050.488-1.12982.595-3.09522.02440.1736-0.0243-0.0685-0.13590.03370.19910.15280.1169-0.16590.2468-0.0249-0.00010.2053-0.01680.165819.8963-11.08638.1419
30.02070.89341.13861.0621.88780.78910.07390.0250.01980.01410.0669-0.0426-0.0032-0.1159-0.11640.2478-0.04320.01150.1970.00090.19233.4883-1.8458-9.2346
41.83720.05372.2851-0.35150.49880.95120.1-0.09630.0021-0.00660.01260.004-0.0447-0.0923-0.08950.1737-0.00670.01110.23940.00980.19-0.1566-3.9472-5.7561
51.10190.7951.76381.39893.18051.99580.033-0.0917-0.0798-0.00450.08320.0604-0.0038-0.239-0.10110.2868-0.04730.00740.21810.02780.16394.1274-29.33254.6051
61.65620.1643.7716-0.3371-0.02663.01540.0746-0.2699-0.005-0.00390.0705-0.0201-0.1289-0.398-0.15460.18920.00640.00950.36860.0280.18640.4997-31.35878.0489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 10
2X-RAY DIFFRACTION2chain BB1 - 10
3X-RAY DIFFRACTION3chain CC1 - 10
4X-RAY DIFFRACTION4chain DD1 - 10
5X-RAY DIFFRACTION5chain EE1 - 10
6X-RAY DIFFRACTION6chain FF1 - 10

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