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- PDB-2vuq: Crystal structure of a human tRNAGly acceptor stem microhelix (de... -

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Basic information

Entry
Database: PDB / ID: 2vuq
TitleCrystal structure of a human tRNAGly acceptor stem microhelix (derived from the gene sequence DG9990) at 1.18 Angstroem resolution
Components
  • 5'-R(*CP*CP*AP*AP*UP*GP*CP)-3'
  • 5'-R(*GP*CP*AP*UP*UP*GP*GP)-3'
KeywordsRNA / CLASS II AMINOACYL-TRNA / SYNTHETASE SYSTEM / TRNA IDENTITY ELEMENTS / GLYCYL-TRNA-SYNTHETASE (GLYRS) / ISOACCEPTORS / HUMAN TRNAGLY / AMINOACYL-TRNA-STEM
Function / homologyRNA
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsEichert, A. / Perbandt, M. / Schreiber, A. / Fuerste, J.P. / Betzel, C. / Erdmann, V.A. / Foerster, C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Crystal Structure of the Human Trnagly Microhelix Isoacceptor G9990 at 1.18 A Resolution
Authors: Eichert, A. / Perbandt, M. / Schreiber, A. / Fuerste, J.P. / Betzel, C. / Erdmann, V.A. / Foerster, C.
History
DepositionMay 29, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_struct_special_symmetry
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-R(*GP*CP*AP*UP*UP*GP*GP)-3'
B: 5'-R(*CP*CP*AP*AP*UP*GP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)4,4182
Polymers4,4182
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-2.5 kcal/mol
Surface area2760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.318, 37.613, 30.465
Angle α, β, γ (deg.)90.00, 112.60, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2015-

HOH

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Components

#1: RNA chain 5'-R(*GP*CP*AP*UP*UP*GP*GP)-3' / HUMAN TRNAGLY MICROHELIX G9990


Mass: 2237.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#2: RNA chain 5'-R(*CP*CP*AP*AP*UP*GP*CP)-3' / HUMAN TRNAGLY MICROHELIX G9990


Mass: 2180.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.07 Å3/Da / Density % sol: 40.21 % / Description: NONE
Crystal growTemperature: 294 K / pH: 6
Details: 10% (V/V) MPD, 40 MM SODIUM CACODYLATE, PH 6.0, 12 MM SPERMINE TETRACHLORIDE, 80 MM POTASSIUM CHLORIDE, EQUILIBRATED AGAINST 35 % (V/V) MPD AT 294 K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9696
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9696 Å / Relative weight: 1
ReflectionResolution: 1.18→50 Å / Num. obs: 12058 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.9
Reflection shellResolution: 1.18→1.22 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 1.8 / % possible all: 87

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Processing

Software
NameVersionClassification
REFMAC5refinement
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V7R

2v7r


Resolution: 1.18→22.25 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.93 / SU B: 1.048 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22806 601 5 %RANDOM
Rwork0.20405 ---
obs0.2052 11449 93.75 %-
Solvent computationSolvent model: NONE
Displacement parametersBiso mean: 11.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.01 Å2
2--0.07 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.18→22.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 292 0 48 340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021325
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6273503
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_restr0.0560.256
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02144
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1620.2109
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2730.2217
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.232
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1120.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0670.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8923461
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.294.5503
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.181→1.212 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 43 -
Rwork0.232 804 -
obs--88.78 %

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