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- PDB-2v7r: Crystal structure of a human tRNAGly microhelix at 1.2 Angstrom r... -

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Basic information

Entry
Database: PDB / ID: 2v7r
TitleCrystal structure of a human tRNAGly microhelix at 1.2 Angstrom resolution
Components(HUMAN TRNAGLY MICROHELIX) x 2
KeywordsRNA / TRNA / ACCEPTOR STEM / GLYCINE / MICROHELIX / IDENTITY / HYDRATION
Function / homologyRNA
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsFoerster, C. / Mankowska, M. / Fuerste, J.P. / Perbandt, M. / Betzel, C. / Erdmann, V.A.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2008
Title: Crystal Structure of a Human Trnagly Microhelix at 1.2 A Resolution.
Authors: Foerster, C. / Mankowska, M. / Fuerste, J.P. / Perbandt, M. / Betzel, C. / Erdmann, V.A.
History
DepositionAug 1, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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

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Assembly

Deposited unit
A: HUMAN TRNAGLY MICROHELIX
B: HUMAN TRNAGLY MICROHELIX


Theoretical massNumber of molelcules
Total (without water)4,4332
Polymers4,4332
Non-polymers00
Water1,53185
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint0 kcal/mol
Surface area3130 Å2
MethodPQS
Unit cell
Length a, b, c (Å)37.120, 37.491, 30.379
Angle α, β, γ (deg.)90.00, 113.02, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2024-

HOH

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Components

#1: RNA chain HUMAN TRNAGLY MICROHELIX


Mass: 2253.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human)
#2: RNA chain HUMAN TRNAGLY MICROHELIX


Mass: 2179.387 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.: 85 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 59.4 % / Description: NONE
Crystal growDetails: 40 MM SODIUM CACODYLATE, PH 6.0, 12 MM SPERMINE TETRA-HCL, 12 MM SODIUM CHLORIDE, 80 MM POTASSIUM CHLORIDE, 10% (V/V) MPD, EQUILIBRATED AGAINST 35% (V/V) MPD AT ROOM TEMPERATURE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8148
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8148 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 11547 / % possible obs: 95.3 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.1
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.24 / % possible all: 93.7

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→14.08 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.421 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.208 568 4.9 %RANDOM
Rwork0.187 ---
obs0.188 10934 95.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.05 Å2
2---0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.2→14.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 293 0 85 378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021326
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7123505
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_restr0.0620.256
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02145
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1650.2126
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2740.2226
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.274
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.218
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_it2.3953468
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6044.5505
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: 1.2→1.23 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.223 40
Rwork0.188 775

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