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- PDB-3r1d: Crystal structure of GC(8BrG)GCGGCGGC duplex -

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Basic information

Entry
Database: PDB / ID: 3r1d
TitleCrystal structure of GC(8BrG)GCGGCGGC duplex
ComponentsRNA (5'-R(*GP*CP*(GRB)P*GP*CP*GP*GP*CP*GP*GP*C)-3')
KeywordsRNA / CGG repeats / fragile X mental retardation / 8-bromoguanosine
Function / homologyBROMIDE ION / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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*(GRB)P*GP*CP*GP*GP*CP*GP*GP*C)-3')
B: RNA (5'-R(*GP*CP*(GRB)P*GP*CP*GP*GP*CP*GP*GP*C)-3')
C: RNA (5'-R(*GP*CP*(GRB)P*GP*CP*GP*GP*CP*GP*GP*C)-3')
D: RNA (5'-R(*GP*CP*(GRB)P*GP*CP*GP*GP*CP*GP*GP*C)-3')
E: RNA (5'-R(*GP*CP*(GRB)P*GP*CP*GP*GP*CP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,28415
Polymers18,3565
Non-polymers92810
Water3,711206
1
A: RNA (5'-R(*GP*CP*(GRB)P*GP*CP*GP*GP*CP*GP*GP*C)-3')
B: RNA (5'-R(*GP*CP*(GRB)P*GP*CP*GP*GP*CP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7907
Polymers7,3422
Non-polymers4485
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-6 kcal/mol
Surface area4240 Å2
MethodPISA
2
C: RNA (5'-R(*GP*CP*(GRB)P*GP*CP*GP*GP*CP*GP*GP*C)-3')
D: RNA (5'-R(*GP*CP*(GRB)P*GP*CP*GP*GP*CP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6305
Polymers7,3422
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-5 kcal/mol
Surface area4200 Å2
MethodPISA
3
E: RNA (5'-R(*GP*CP*(GRB)P*GP*CP*GP*GP*CP*GP*GP*C)-3')
hetero molecules

E: RNA (5'-R(*GP*CP*(GRB)P*GP*CP*GP*GP*CP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7266
Polymers7,3422
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area1120 Å2
ΔGint-8 kcal/mol
Surface area4260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.565, 28.612, 61.833
Angle α, β, γ (deg.)90.00, 117.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-214-

HOH

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Components

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


Mass: 3671.106 Da / Num. of mol.: 5 / Source method: obtained synthetically / Details: This sequence is found in human mRNA
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.52 Å3/Da / Density % sol: 51.25 %
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: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8126 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 22, 2005
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8126 Å / Relative weight: 1
ReflectionResolution: 1.45→20 Å / Num. all: 32941 / Num. obs: 32941 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 21.2 Å2 / Rsym value: 0.112 / Net I/σ(I): 10
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 6.3 % / Num. unique all: 1627 / Rsym value: 0.62 / % 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 / Resolution: 1.45→19.967 Å / SU ML: 0.25 / σ(F): 1.33 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2702 671 2.06 %RANDOM
Rwork0.2321 ---
obs0.2329 32646 98.92 %-
all-32646 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.966 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.1309 Å2-0 Å20.0486 Å2
2--0.102 Å2-0 Å2
3---0.0289 Å2
Refinement stepCycle: LAST / Resolution: 1.45→19.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1195 42 206 1443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061846
X-RAY DIFFRACTIONf_angle_d1.2822897
X-RAY DIFFRACTIONf_dihedral_angle_d15.516730
X-RAY DIFFRACTIONf_chiral_restr0.051364
X-RAY DIFFRACTIONf_plane_restr0.00574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.5620.31481200.30496357X-RAY DIFFRACTION99
1.562-1.71910.30181380.24116397X-RAY DIFFRACTION100
1.7191-1.96760.29011340.24866277X-RAY DIFFRACTION98
1.9676-2.47830.30931320.24076370X-RAY DIFFRACTION99
2.4783-19.96840.24291470.21366574X-RAY DIFFRACTION99

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