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- PDB-3sj2: A Crystal Structure of a Model of the Repeating r(CGG) Transcript... -

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Basic information

Entry
Database: PDB / ID: 3sj2
TitleA Crystal Structure of a Model of the Repeating r(CGG) Transcript Found in Fragile X Syndrome
Components
  • RNA (5'-R(*UP*UP*GP*GP*GP*CP*CP*GP*GP*CP*GP*GP*CP*GP*GP*GP*UP*CP*C)-3')
  • RNA (5'-R(P*GP*GP*GP*CP*CP*GP*GP*CP*GP*GP*CP*GP*GP*GP*UP*CP*C)-3')
KeywordsRNA / Trinucleotide disorders / Fragile X-syndrome
Function / homologyACETATE ION / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsKumar, A. / Pengfei, F. / Park, H. / Nettles, K. / Guo, M. / Disney, M.D.
CitationJournal: Chembiochem / Year: 2011
Title: A Crystal Structure of a Model of the Repeating r(CGG) Transcript Found in Fragile X Syndrome.
Authors: Kumar, A. / Fang, P. / Park, H. / Guo, M. / Nettles, K.W. / Disney, M.D.
History
DepositionJun 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references
Revision 1.2Feb 28, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*UP*UP*GP*GP*GP*CP*CP*GP*GP*CP*GP*GP*CP*GP*GP*GP*UP*CP*C)-3')
B: RNA (5'-R(P*GP*GP*GP*CP*CP*GP*GP*CP*GP*GP*CP*GP*GP*GP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8194
Polymers11,7012
Non-polymers1182
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-11 kcal/mol
Surface area6770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.660, 32.320, 69.442
Angle α, β, γ (deg.)90.00, 108.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 6156.689 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain RNA (5'-R(P*GP*GP*GP*CP*CP*GP*GP*CP*GP*GP*CP*GP*GP*GP*UP*CP*C)-3')


Mass: 5544.357 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 51.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Potassium Chloride, 0.01 M Magnesium Chloride, 0.05 M Tris.HCl, 30%(v/v)PEG 400, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 6, 2011
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.36→27.56 Å / Num. all: 25014 / Num. obs: 24111 / % possible obs: 98.64 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 25.38 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.36-1.46199.9
1.46-1.56199.9
1.56-1.68199.6
1.68-1.84199.7
1.84-2.06199.3
2.06-2.38198.9
2.38-2.92198
2.92-4.12196.1
4.12-27.56193.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→27.543 Å / SU ML: 0.13 / σ(F): 0 / Phase error: 18.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1851 1941 8.05 %random
Rwork0.1545 ---
obs0.1571 22170 95.21 %-
all-24111 --
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.225 Å2 / ksol: 0.411 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3287 Å20 Å2-1.0978 Å2
2---0.8803 Å2-0 Å2
3---0.5515 Å2
Refinement stepCycle: LAST / Resolution: 1.36→27.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 777 8 277 1062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005873
X-RAY DIFFRACTIONf_angle_d0.7831358
X-RAY DIFFRACTIONf_dihedral_angle_d13.802425
X-RAY DIFFRACTIONf_chiral_restr0.054179
X-RAY DIFFRACTIONf_plane_restr0.00838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.39470.2561220.20421467X-RAY DIFFRACTION88
1.3947-1.43240.27341320.1821472X-RAY DIFFRACTION91
1.4324-1.47460.23561340.1571569X-RAY DIFFRACTION93
1.4746-1.52220.17171330.14491523X-RAY DIFFRACTION94
1.5222-1.57660.18821310.12491592X-RAY DIFFRACTION96
1.5766-1.63970.16171400.12261594X-RAY DIFFRACTION96
1.6397-1.71430.18181450.12221602X-RAY DIFFRACTION97
1.7143-1.80470.15671400.13261628X-RAY DIFFRACTION98
1.8047-1.91770.17911460.14211621X-RAY DIFFRACTION98
1.9177-2.06570.18211460.14681628X-RAY DIFFRACTION98
2.0657-2.27350.19711400.15911633X-RAY DIFFRACTION98
2.2735-2.60230.1821440.16261622X-RAY DIFFRACTION97
2.6023-3.27780.21521480.17271626X-RAY DIFFRACTION96
3.2778-27.54870.1561400.15871593X-RAY DIFFRACTION92

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