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- PDB-3rg5: Crystal Structure of Mouse tRNA(Sec) -

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Basic information

Entry
Database: PDB / ID: 3rg5
TitleCrystal Structure of Mouse tRNA(Sec)
ComponentstRNA(Sec)
KeywordsRNA / Metal binding by RNA / RNA hydration / structural flexibility / tRNASec / tRNA fold / translation / SerRS / SecS / PSTK
Function / homologyACETATE ION / : / RNA / RNA (> 10)
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWahl, M.C. / Ganichkin, O.M. / Anedchenko, E.A.
CitationJournal: Plos One / Year: 2011
Title: Crystal structure analysis reveals functional flexibility in the selenocysteine-specific tRNA from mouse.
Authors: Ganichkin, O.M. / Anedchenko, E.A. / Wahl, M.C.
History
DepositionApr 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA(Sec)
B: tRNA(Sec)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7438
Polymers55,2492
Non-polymers4946
Water3,513195
1
A: tRNA(Sec)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8714
Polymers27,6241
Non-polymers2473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA(Sec)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8714
Polymers27,6241
Non-polymers2473
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-38 kcal/mol
Surface area28350 Å2
MethodPISA
4
A: tRNA(Sec)
hetero molecules

B: tRNA(Sec)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7438
Polymers55,2492
Non-polymers4946
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area1580 Å2
ΔGint-35 kcal/mol
Surface area28840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.872, 96.055, 71.841
Angle α, β, γ (deg.)90.00, 105.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain tRNA(Sec)


Mass: 27624.295 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthesized by in vitro transcription / Source: (synth.) Mus musculus (house mouse) / References: GenBank: 3RG5
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.95 Å3/Da / Density % sol: 58.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 0.1 M MES, pH 5.2, 10 mM magnesium acetate, 2.0 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 42189 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.047 / Net I/σ(I): 19.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.2 / Rsym value: 0.807 / % possible all: 90.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: human tRNA(Sec)

Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.988 / SU ML: 0.134 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25284 2124 5 %RANDOM
Rwork0.21539 ---
obs0.2173 40040 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.3 Å20 Å20.74 Å2
2--1.7 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3658 30 195 3883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214109
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.74936391
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2860
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021776
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3781.59
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.62626
X-RAY DIFFRACTIONr_scbond_it1.60234100
X-RAY DIFFRACTIONr_scangle_it2.3464.56385
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 172 -
Rwork0.377 2700 -
obs--90.06 %

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