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- PDB-3a3a: Crystal structure of human selenocystine tRNA -

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Basic information

Entry
Database: PDB / ID: 3a3a
TitleCrystal structure of human selenocystine tRNA
Componentsselenocysteine tRNA
KeywordsRNA / tRNA
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsItoh, Y. / Chiba, S. / Sekine, S.I. / Yokoyama, S.
CitationJournal: Nucleic Acids Res. / Year: 2009
Title: Crystal structure of human selenocysteine tRNA.
Authors: Itoh, Y. / Chiba, S. / Sekine, S. / Yokoyama, S.
History
DepositionJun 11, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 18, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_src_syn / struct_conn / struct_ref
Item: _entity.src_method / _ndb_struct_conf_na.feature ..._entity.src_method / _ndb_struct_conf_na.feature / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.hbond_type_12 / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair.stagger / _ndb_struct_na_base_pair_step.inclination / _ndb_struct_na_base_pair_step.tilt / _ndb_struct_na_base_pair_step.tip / _struct_ref.pdbx_align_begin
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: selenocysteine tRNA


Theoretical massNumber of molelcules
Total (without water)28,9081
Polymers28,9081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.949, 51.573, 81.365
Angle α, β, γ (deg.)90.00, 101.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain selenocysteine tRNA


Mass: 28908.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: RNA was prepared by in vitro transcription with T7 RNA polymerase.
Production host: cell-free synthesis (others)

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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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.1
Details: 32% PEG 1500, 0.1M sodium acetate-HCl pH 4.1, 140mM lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2008 / Details: monochromator
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. all: 6032 / Num. obs: 5833 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 18
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.53 / Num. unique all: 608 / Rsym value: 0.39 / % possible all: 85.9

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2TRA, 6TNA

2tra

6tna


Resolution: 3.1→36.13 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 2615319.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.314 258 4.5 %RANDOM
Rwork0.254 ---
obs0.254 5781 97 %-
all-5965 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 18.6706 Å2 / ksol: 0.1 e/Å3
Displacement parametersBiso mean: 115 Å2
Baniso -1Baniso -2Baniso -3
1-5.19 Å20 Å2-55.5 Å2
2---16.71 Å20 Å2
3---11.52 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.74 Å0.51 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.72 Å
Refinement stepCycle: LAST / Resolution: 3.1→36.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1829 0 0 1829
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_deg0.92
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d13
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.27
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: 3.1→3.29 Å / Rfactor Rfree error: 0.055 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 41 4.6 %
Rwork0.422 841 -
obs-649 89.8 %
Xplor fileSerial no: 1 / Param file: dna-rna_rep.param / Topol file: dna-rna.top

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