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- PDB-3r1c: Crystal structure of GCGGCGGC duplex -

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Basic information

Entry
Database: PDB / ID: 3r1c
TitleCrystal structure of GCGGCGGC duplex
ComponentsRNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
KeywordsRNA / CGG repeats / fragile X mental retardation
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0531 Å
AuthorsKiliszek, A. / Kierzek, R. / Krzyzosiak, W.J. / Rypniewski, W.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Crystal structures of CGG RNA repeats with implications for fragile X-associated tremor ataxia syndrome.
Authors: Kiliszek, A. / Kierzek, R. / Krzyzosiak, W.J. / Rypniewski, W.
History
DepositionMar 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 14, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 13, 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 / 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 / _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

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Assembly

Deposited unit
A: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
B: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
C: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
D: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
E: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
F: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
G: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
H: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
I: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
J: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
K: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
L: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
M: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
N: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
O: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
P: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
Q: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
R: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
S: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
Y: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
T: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
U: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
W: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
X: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
V: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
Z: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
a: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
b: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
c: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
d: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
e: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
f: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
g: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
h: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
i: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
j: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,15143
Polymers93,47836
Non-polymers6727
Water9,440524
1
A: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
B: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,1932
Polymers5,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-5 kcal/mol
Surface area3130 Å2
MethodPISA
2
C: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
D: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,1932
Polymers5,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-5 kcal/mol
Surface area3130 Å2
MethodPISA
3
E: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
F: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,1932
Polymers5,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-5 kcal/mol
Surface area3120 Å2
MethodPISA
4
G: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
H: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,1932
Polymers5,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-5 kcal/mol
Surface area3130 Å2
MethodPISA
5
I: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
J: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,1932
Polymers5,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-5 kcal/mol
Surface area3120 Å2
MethodPISA
6
K: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
L: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,1932
Polymers5,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-5 kcal/mol
Surface area3130 Å2
MethodPISA
7
M: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
N: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,1932
Polymers5,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-5 kcal/mol
Surface area3120 Å2
MethodPISA
8
O: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
P: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,1932
Polymers5,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-5 kcal/mol
Surface area3140 Å2
MethodPISA
9
Q: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
R: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,1932
Polymers5,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-5 kcal/mol
Surface area3120 Å2
MethodPISA
10
S: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
Y: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2893
Polymers5,1932
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-14 kcal/mol
Surface area3170 Å2
MethodPISA
11
T: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
U: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,1932
Polymers5,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-5 kcal/mol
Surface area3140 Å2
MethodPISA
12
W: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
X: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3854
Polymers5,1932
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-28 kcal/mol
Surface area3170 Å2
MethodPISA
13
V: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
Z: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,1932
Polymers5,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-5 kcal/mol
Surface area3140 Å2
MethodPISA
14
a: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
b: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2893
Polymers5,1932
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-14 kcal/mol
Surface area3190 Å2
MethodPISA
15
c: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
d: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3854
Polymers5,1932
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-25 kcal/mol
Surface area3220 Å2
MethodPISA
16
e: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
f: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2893
Polymers5,1932
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-15 kcal/mol
Surface area3160 Å2
MethodPISA
17
g: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
h: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,1932
Polymers5,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-5 kcal/mol
Surface area3150 Å2
MethodPISA
18
i: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')
j: RNA (5'-R(*GP*CP*GP*GP*CP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)5,1932
Polymers5,1932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-5 kcal/mol
Surface area3130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.697, 76.891, 85.398
Angle α, β, γ (deg.)89.98, 88.61, 77.29
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 2596.617 Da / Num. of mol.: 36 / Source method: obtained synthetically / Details: This sequence is found in human mRNA
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.72 Å3/Da / Density % sol: 54.77 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10 mM MgCl2, cacodylate, 1.0 M Li2SO4, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.92001 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 16, 2010
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92001 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 60328 / Num. obs: 60328 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 33 Å2 / Rsym value: 0.093 / Net I/σ(I): 17
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 3027 / Rsym value: 0.488 / % possible all: 97.5

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Processing

Software
NameClassification
MAR345data collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3R1E

3r1e


Resolution: 2.0531→19.356 Å / SU ML: 0.36 / σ(F): 1.96 / Phase error: 28.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2571 3038 5.06 %RANDOM
Rwork0.2156 ---
obs0.2177 60089 97.7 %-
all-60089 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.71 Å2 / ksol: 0.387 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.571 Å20.9279 Å2-0.8488 Å2
2---0.0049 Å20.5533 Å2
3---0.5759 Å2
Refinement stepCycle: LAST / Resolution: 2.0531→19.356 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 6192 35 524 6751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057070
X-RAY DIFFRACTIONf_angle_d1.14511020
X-RAY DIFFRACTIONf_dihedral_angle_d13.982798
X-RAY DIFFRACTIONf_chiral_restr0.0441429
X-RAY DIFFRACTIONf_plane_restr0.003293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0531-2.08510.31121160.23532500X-RAY DIFFRACTION90
2.0851-2.11930.31051190.25082563X-RAY DIFFRACTION98
2.1193-2.15580.30421460.2532507X-RAY DIFFRACTION97
2.1558-2.19490.28551570.2342632X-RAY DIFFRACTION98
2.1949-2.23710.2991230.24022583X-RAY DIFFRACTION98
2.2371-2.28270.30741190.23462584X-RAY DIFFRACTION98
2.2827-2.33220.29111390.23682669X-RAY DIFFRACTION98
2.3322-2.38640.29751360.2292567X-RAY DIFFRACTION98
2.3864-2.4460.29891440.23662602X-RAY DIFFRACTION98
2.446-2.5120.31641380.23262613X-RAY DIFFRACTION98
2.512-2.58570.26971300.24612582X-RAY DIFFRACTION98
2.5857-2.6690.31321490.24312635X-RAY DIFFRACTION98
2.669-2.76410.2881220.24242579X-RAY DIFFRACTION98
2.7641-2.87440.29491570.23072634X-RAY DIFFRACTION98
2.8744-3.00480.23981450.21442571X-RAY DIFFRACTION98
3.0048-3.16260.24561380.20292593X-RAY DIFFRACTION98
3.1626-3.35970.24411410.20832635X-RAY DIFFRACTION98
3.3597-3.61760.24831370.1982597X-RAY DIFFRACTION98
3.6176-3.97880.20461440.17342603X-RAY DIFFRACTION98
3.9788-4.5480.17161460.15872607X-RAY DIFFRACTION99
4.548-5.70560.1731490.15212628X-RAY DIFFRACTION99
5.7056-19.35690.19421430.17672567X-RAY DIFFRACTION97

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