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- PDB-430d: STRUCTURE OF SARCIN/RICIN LOOP FROM RAT 28S RRNA -

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Basic information

Entry
Database: PDB / ID: 430d
TitleSTRUCTURE OF SARCIN/RICIN LOOP FROM RAT 28S RRNA
ComponentsSARCIN/RICIN LOOP FROM RAT 28S R-RNA
KeywordsRNA / U-RNA / DOUBLE HELIX / HAIRPIN / BLUNT STEM / TETRALOOP MISMATCHED / BASE TRIPLE / RIBONUCLEIC ACID
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD PHASING METHOD / Resolution: 2.1 Å
AuthorsCorrell, C.C. / Munishkin, A. / Chan, Y.L. / Ren, Z. / Wool, I.G. / Steitz, T.A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Crystal structure of the ribosomal RNA domain essential for binding elongation factors.
Authors: Correll, C.C. / Munishkin, A. / Chan, Y.L. / Ren, Z. / Wool, I.G. / Steitz, T.A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: The Conformation of the Sarcin/Ricin Loop from 28S Ribosomal RNA
Authors: Szewczak, A.A. / Moore, P.B. / Chan, Y.L. / Wool, I.G.
#2: Journal: J.Mol.Biol. / Year: 1995
Title: The Sarcin/Ricin Loop, a Modular RNA
Authors: Szewczak, A.A. / Moore, P.B.
#3: Journal: Biophys.J. / Year: 1998
Title: Comparison of the Crystal and Solution Structure of Two RNA Oligonucleotides
Authors: Rife, J.P. / Stallings, S.C. / Correll, C.C. / Dallas, A. / Steitz, T.A. / Moore, P.B.
History
DepositionOct 4, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Oct 7, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 3, 2017Group: Source and taxonomy / Structure summary
Revision 1.4Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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 LOOP FROM RAT 28S R-RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,67410
Polymers9,4561
Non-polymers2199
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.830, 56.830, 107.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Cell settinghexagonal
Space group name H-MP6122

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Components

#1: RNA chain SARCIN/RICIN LOOP FROM RAT 28S R-RNA


Mass: 9455.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.68 Å3/Da / Density % sol: 54.17 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
25 mM1dropMgCl2
350 mMMOPS1drop
43.0-3.2 Mammonium sulfate1reservoir
550 mMMOPS1reservoir
620 mM1reservoirMgCl2
71 mMspermine1reservoir
82 mM1reservoirCoCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorType: ADSC / Detector: CCD / Date: Nov 15, 1997 / Details: SILICON 111 BENDING MIRRO
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 5854 / % possible obs: 89.6 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 59.6 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 32.5
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.217 / % possible all: 88.8
Reflection
*PLUS
Num. obs: 6036 / % possible obs: 92.7 % / Num. measured all: 22518

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD PHASING METHOD / Resolution: 2.1→30 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 30991867.71 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.33 646 9.9 %RANDOM
Rwork0.28 ---
obs0.28 6036 92.7 %-
Displacement parametersBiso mean: 60.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å23.31 Å20 Å2
2--1.48 Å20 Å2
3----2.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 621 10 9 640
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d30.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.36
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.1→2.16 Å / Rfactor Rfree error: 0.092 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.593 48 10.4 %
Rwork0.519 414 -
obs--90.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1DNA-RNA-MULTI-ENDO.PARAMDNA-RNA-MULTI-ENDO.TOP
X-RAY DIFFRACTION2MG.PARAMMG.PARAM
X-RAY DIFFRACTION3BR.PARAMBR.PARAM
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 30 Å / Rfactor obs: 0.28 / Rfactor Rfree: 0.33
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg30.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.36
LS refinement shell
*PLUS
Highest resolution: 2.1 Å

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