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- PDB-3dvz: Crystal Structure of the Sarcin/Ricin Domain from E. coli 23 S rRNA -

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Basic information

Entry
Database: PDB / ID: 3dvz
TitleCrystal Structure of the Sarcin/Ricin Domain from E. coli 23 S rRNA
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 1.2Oct 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_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: Sarcin/Ricin Domain from E. Coli 23 S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8362
Polymers8,7441
Non-polymers921
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.540, 29.540, 76.190
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: 8744.255 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.: 148 / 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: 35.29 %
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: 1 Å / Num. obs: 33970 / % possible obs: 96.6 % / Redundancy: 11.8 % / Biso Wilson estimate: 13.872 Å2 / Rsym value: 0.04 / Net I/σ(I): 28.37
Reflection shellResolution: 1→1.1 Å / Mean I/σ(I) obs: 3.9 / Num. measured obs: 59134 / Num. unique obs: 7559 / Rsym value: 0.506 / % possible all: 86.4

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Processing

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

1q9a


Resolution: 1→27.542 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.12 / σ(F): 2.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.165 1723 5.07 %RANDOM
Rwork0.149 ---
obs0.15 33970 96.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.988 Å2 / ksol: 0.456 e/Å3
Displacement parametersBiso max: 39.14 Å2 / Biso mean: 15.434 Å2 / Biso min: 7.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.594 Å2-0 Å20 Å2
2---0.594 Å2-0 Å2
3---1.188 Å2
Refinement stepCycle: LAST / Resolution: 1→27.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 579 6 148 733
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003718
X-RAY DIFFRACTIONf_angle_d0.9411125
X-RAY DIFFRACTIONf_chiral_restr0.044148
X-RAY DIFFRACTIONf_plane_restr0.00429
X-RAY DIFFRACTIONf_dihedral_angle_d19.728302
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1-1.0290.2491000.2342091219175
1.029-1.0630.2351150.2162458257388
1.063-1.1010.1911440.172685282997
1.101-1.1450.1681490.14327582907100
1.145-1.1970.1611580.14127712929100
1.197-1.260.1631520.1427712923100
1.26-1.3390.1741310.14428072938100
1.339-1.4420.171510.14627532904100
1.442-1.5870.1591680.14727702938100
1.587-1.8170.141410.12728012942100
1.817-2.2890.1421630.14727802943100
2.289-27.5530.1661510.14728022953100

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