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- PDB-7eqj: crystal structure of E. coli Valine tRNA -

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Basic information

Entry
Database: PDB / ID: 7eqj
Titlecrystal structure of E. coli Valine tRNA
ComponentsRNA (76-MER)
KeywordsRNA / tRNA
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.043 Å
AuthorsKim, J. / Jeong, H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Rna / Year: 2021
Title: Unique anticodon loop conformation with the flipped-out wobble nucleotide in the crystal structure of unbound tRNA Val .
Authors: Jeong, H. / Kim, J.
History
DepositionMay 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (76-MER)
B: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,20512
Polymers48,9672
Non-polymers23810
Water2,774154
1
A: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6016
Polymers24,4841
Non-polymers1185
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-12 kcal/mol
Surface area12580 Å2
MethodPISA
2
B: RNA (76-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6046
Polymers24,4841
Non-polymers1205
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.541, 33.059, 131.797
Angle α, β, γ (deg.)90.000, 98.150, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain RNA (76-MER)


Mass: 24483.572 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K-12
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsThe sequence of tRNA is originiated from Escherichia coli str. K-12 substr. MG1655 (GenBank: U00096.3)

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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: 2.37 Å3/Da / Density % sol: 48.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.05M Magnesium chloride hexahydrate 0.1M HEPES pH 7.5 30%(v/v) polyethylene glycol monomethyl ether 550 30%(v/v) 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97926 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.043→30 Å / Num. obs: 28804 / % possible obs: 97.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 37.86 Å2 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.041 / Rrim(I) all: 0.108 / Χ2: 0.679 / Net I/σ(I): 4.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.095.10.82713090.7750.3660.9080.38788.9
2.09-2.125.40.77113450.7830.3360.8440.38893.7
2.12-2.165.90.67713790.8510.2860.7370.39595.5
2.16-2.216.40.59414550.8910.2450.6440.39697.4
2.21-2.266.60.52814120.9160.2170.5710.40197.6
2.26-2.316.80.45214080.9170.1840.4890.40297.4
2.31-2.376.80.39914670.9430.1620.4320.40498.1
2.37-2.436.90.33214370.960.1350.3590.41898.3
2.43-2.56.70.28514160.9660.1180.3090.4198.3
2.5-2.586.50.25614490.9710.1090.2780.42898.4
2.58-2.676.20.20514550.9770.090.2250.46398.3
2.67-2.786.40.17714470.9810.0760.1930.48998.5
2.78-2.917.10.13714240.9930.0550.1470.55898.5
2.91-3.067.10.10214860.9950.040.110.71598.8
3.06-3.256.90.08214530.9960.0330.0881.00898.8
3.25-3.56.70.07514840.9960.0310.0811.15398.9
3.5-3.866.70.0714670.9960.0290.0761.14399
3.86-4.416.30.06414510.9970.0270.071.17897.4
4.41-5.555.50.05914890.9960.0280.0651.33796.9
5.55-306.70.05215710.9980.0210.0571.28299.1

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZW4

5zw4


Resolution: 2.043→29.488 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 1494 5.19 %
Rwork0.2044 27277 -
obs0.2061 28771 97.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.67 Å2 / Biso mean: 41.6289 Å2 / Biso min: 21.58 Å2
Refinement stepCycle: final / Resolution: 2.043→29.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3221 10 154 3385
Biso mean--41.07 34.06 -
Num. residues----151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053597
X-RAY DIFFRACTIONf_angle_d0.9785603
X-RAY DIFFRACTIONf_chiral_restr0.042755
X-RAY DIFFRACTIONf_plane_restr0.008151
X-RAY DIFFRACTIONf_dihedral_angle_d12.2471806
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0433-2.10920.2981040.2705219787
2.1092-2.18450.32971450.2616243096
2.1845-2.2720.26151270.2537244197
2.272-2.37530.31241500.2395248298
2.3753-2.50050.31571220.2431250898
2.5005-2.65710.27281500.2631247698
2.6571-2.86210.32111240.2853250698
2.8621-3.14980.25331250.2276255799
3.1498-3.60490.19931610.1759249399
3.6049-4.53910.20121610.1646252698
4.5391-29.4880.19781250.1651266198

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