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- PDB-3dw7: Crystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rR... -

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Basic information

Entry
Database: PDB / ID: 3dw7
TitleCrystal Structure of the Sarcin/Ricin Domain from E. COLI 23 S rRNA, U2656-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: 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
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)8,8211
Polymers8,8211
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.550, 29.550, 76.210
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: 8821.242 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 1.89 Å3/Da / Density % sol: 34.78 %
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: 0.9791 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: 0.9791 Å / Relative weight: 1
ReflectionHighest resolution: 1 Å / Num. obs: 66643 / % possible obs: 95.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 11.643 Å2 / Rsym value: 0.059 / Net I/σ(I): 15.24
Reflection shellResolution: 1→1.1 Å / Mean I/σ(I) obs: 2.5 / Num. measured obs: 47856 / Num. unique obs: 14613 / Rsym value: 0.456 / % possible all: 84.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementResolution: 1→20.151 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.1 / σ(F): 1.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.17 3345 5.02 %random
Rwork0.153 ---
obs0.154 66643 95.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.823 Å2 / ksol: 0.454 e/Å3
Displacement parametersBiso max: 46.79 Å2 / Biso mean: 14.405 Å2 / Biso min: 6.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.942 Å2-0 Å20 Å2
2---1.942 Å2-0 Å2
3---0.572 Å2
Refinement stepCycle: LAST / Resolution: 1→20.151 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 580 0 156 736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004744
X-RAY DIFFRACTIONf_angle_d1.1041166
X-RAY DIFFRACTIONf_chiral_restr0.052152
X-RAY DIFFRACTIONf_plane_restr0.00630
X-RAY DIFFRACTIONf_dihedral_angle_d28.169335
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1-1.0140.319830.3061630171359
1.014-1.0290.282940.2632033212773
1.029-1.0460.241250.242355248085
1.046-1.0630.271900.2172586267691
1.063-1.0810.1941130.1932637275097
1.081-1.1010.1481280.1782813294199
1.101-1.1220.1621540.16327482902100
1.122-1.1450.1611390.15727322871100
1.145-1.170.1731610.15427622923100
1.17-1.1970.1821520.15427332885100
1.197-1.2270.1661490.14327752924100
1.227-1.260.1491490.14327652914100
1.26-1.2970.1871240.14727842908100
1.297-1.3390.1791480.14627632911100
1.339-1.3870.171530.14327302883100
1.387-1.4420.1631430.15127192862100
1.442-1.5080.1641440.15727922936100
1.508-1.5870.1561610.14727252886100
1.587-1.6870.1531760.12227142890100
1.687-1.8170.121340.13127932927100
1.817-1.9990.1511570.14327442901100
1.999-2.2880.1931760.1572702287899
2.288-2.8820.1971470.1672716286399
2.882-20.1550.1521450.1352547269293

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