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- PDB-3dw5: Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23S rRN... -

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Basic information

Entry
Database: PDB / ID: 3dw5
TitleCrystal Structure of the Sarcin/Ricin Domain from E. COLI 23S rRNA, U2656-OCH3 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: 0.96 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: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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


Theoretical massNumber of molelcules
Total (without water)8,7581
Polymers8,7581
Non-polymers00
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.560, 29.560, 76.160
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: 8758.282 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 35.25 %
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: X06SA / Wavelength: 0.85 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionHighest resolution: 0.96 Å / Num. obs: 39656 / % possible obs: 99.8 % / Redundancy: 11.9 % / Biso Wilson estimate: 12.625 Å2 / Rsym value: 0.032 / Net I/σ(I): 34.5
Reflection shellResolution: 0.96→0.97 Å / Mean I/σ(I) obs: 3.1 / Num. measured obs: 9571 / Num. unique obs: 1123 / Rsym value: 0.634 / % possible all: 92.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
RemDAqdata collection
XDSdata reduction
MOLREPphasing
RefinementStarting model: 1q9a

1q9a


Resolution: 0.96→27.557 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.09 / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.165 1995 5.03 %random
Rwork0.149 ---
obs0.15 39656 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.753 Å2 / ksol: 0.436 e/Å3
Displacement parametersBiso max: 35.27 Å2 / Biso mean: 14.204 Å2 / Biso min: 7.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å20 Å2
2---0.25 Å2-0 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 0.96→27.557 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 580 0 146 726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004704
X-RAY DIFFRACTIONf_angle_d1.1411099
X-RAY DIFFRACTIONf_chiral_restr0.054142
X-RAY DIFFRACTIONf_plane_restr0.00629
X-RAY DIFFRACTIONf_dihedral_angle_d31.317309
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.96-0.9840.2411360.22623275997
0.984-1.0110.191360.17626642800100
1.011-1.040.1811430.1626822825100
1.04-1.0740.1581310.15127292860100
1.074-1.1120.1631510.14126522803100
1.112-1.1570.1651370.13927102847100
1.157-1.2090.1471460.1426732819100
1.209-1.2730.1391390.1427252864100
1.273-1.3530.1431400.14227022842100
1.353-1.4570.171440.14726722816100
1.457-1.6040.1461370.14127102847100
1.604-1.8360.1541550.13127082863100
1.836-2.3130.1681550.15926822837100
2.313-27.5690.1681450.14927292874100

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