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- PDB-3dw6: Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rR... -

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Basic information

Entry
Database: PDB / ID: 3dw6
TitleCrystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2650-SECH3 modified
ComponentsSarcin/Ricin Domain from E. Coli 23 S rRNA
KeywordsRNA / Sarcin Ricin Loop
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1 Å
AuthorsOlieric, V. / Rieder, U. / Lang, K. / Serganov, A. / Schulze-Briese, C. / Micura, R. / Dumas, P. / Ennifar, E.
CitationJournal: Rna / Year: 2009
Title: A fast selenium derivatization strategy for crystallization and phasing of RNA structures.
Authors: Olieric, V. / Rieder, U. / Lang, K. / Serganov, A. / Schulze-Briese, C. / Micura, R. / Dumas, P. / Ennifar, E.
History
DepositionJul 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Sarcin/Ricin Domain from E. Coli 23 S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9132
Polymers8,8211
Non-polymers921
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.600, 29.600, 76.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: RNA chain Sarcin/Ricin Domain from E. Coli 23 S rRNA


Mass: 8821.241 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 1.9 Å3/Da / Density % sol: 35.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.2 M (NH4)2SO4, 50 mM K-MOPS pH 7.0, 10 mM MgCl2, 10 mM MnCl2, vapor diffusion, hanging drop, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2K-MOPS11
3MgCl211
4MnCl211
5H2O11
6(NH4)2SO412
7K-MOPS12
8MgCl212
9MnCl212
10H2O12

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97916 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionHighest resolution: 1 Å / Num. obs: 64959 / % possible obs: 92.5 % / Redundancy: 6.3 % / Biso Wilson estimate: 11.318 Å2 / Rsym value: 0.054 / Net I/σ(I): 16.99
Reflection shellResolution: 1→1.1 Å / Mean I/σ(I) obs: 2.8 / Num. measured obs: 45575 / Num. unique obs: 12469 / Rsym value: 0.417 / % possible all: 71.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementResolution: 1→20.189 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.07 / σ(F): 1.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.149 3256 5.01 %random
Rwork0.131 ---
obs0.132 64959 92.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.316 Å2 / ksol: 0.46 e/Å3
Displacement parametersBiso max: 41.07 Å2 / Biso mean: 13.601 Å2 / Biso min: 7.45 Å2
Baniso -1Baniso -2Baniso -3
1--2.191 Å2-0 Å20 Å2
2---2.191 Å2-0 Å2
3---0.957 Å2
Refinement stepCycle: LAST / Resolution: 1→20.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 580 6 184 770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005666
X-RAY DIFFRACTIONf_angle_d1.2681044
X-RAY DIFFRACTIONf_chiral_restr0.055131
X-RAY DIFFRACTIONf_plane_restr0.01227
X-RAY DIFFRACTIONf_dihedral_angle_d26.164293
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1-1.0150.319690.2991493156251
1.015-1.0310.279930.251703179660
1.031-1.0480.204780.221961203966
1.048-1.0660.196840.1982288237277
1.066-1.0850.1971220.1792471259385
1.085-1.1060.1771180.1582775289395
1.106-1.1290.1821780.1472857303599
1.129-1.1530.1511560.13828212977100
1.153-1.180.1521820.12329393121100
1.18-1.2090.1381610.12328723033100
1.209-1.2420.1281370.11529183055100
1.242-1.2790.1231450.11429233068100
1.279-1.320.1531680.12328643032100
1.32-1.3670.171720.11828963068100
1.367-1.4220.1271410.12129033044100
1.422-1.4870.1251780.11829013079100
1.487-1.5650.1331500.12628973047100
1.565-1.6630.1421350.11129003035100
1.663-1.7910.1241710.11128543025100
1.791-1.9710.151720.12228913063100
1.971-2.2560.1531490.13728893038100
2.256-2.8420.191650.152858302399
2.842-20.1930.1171320.1192829296197

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