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- PDB-5xz1: Crystal structure of the Homo Sapiens cytoplasmic ribosomal decod... -

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Basic information

Entry
Database: PDB / ID: 5xz1
TitleCrystal structure of the Homo Sapiens cytoplasmic ribosomal decoding site in complex with G418
ComponentsRNA (5'-R(*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')
KeywordsRNA / ribosome / decoding site / G418
Function / homologyGENETICIN / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.008 Å
AuthorsKanazawa, H. / Tsurumi, N. / Kondo, J.
CitationJournal: To Be Published
Title: Structural studies of aminoglycoside antibiotics G418 and its derivatives with readthrough activities
Authors: Kanazawa, H. / Tsurumi, N. / Baasov, T. / Kondo, J.
History
DepositionJul 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')
B: RNA (5'-R(*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')
C: RNA (5'-R(*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')
D: RNA (5'-R(*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1838
Polymers28,1974
Non-polymers1,9864
Water45025
1
A: RNA (5'-R(*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')
B: RNA (5'-R(*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0924
Polymers14,0982
Non-polymers9932
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-45 kcal/mol
Surface area8090 Å2
MethodPISA
2
C: RNA (5'-R(*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')
D: RNA (5'-R(*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0924
Polymers14,0982
Non-polymers9932
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-52 kcal/mol
Surface area7840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.399, 32.528, 96.484
Angle α, β, γ (deg.)90.000, 95.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain
RNA (5'-R(*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')


Mass: 7049.243 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-GET / GENETICIN / G418


Mass: 496.552 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H40N4O10 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2-methyl-2,4-pentandiol, Sodium cacodylate, Spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.01→48.013 Å / Num. obs: 5988 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.285 % / Biso Wilson estimate: 54.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.084 / Χ2: 0.91 / Net I/σ(I): 12.46 / Num. measured all: 19672 / Scaling rejects: 32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.01-3.093.0050.3562.5312384304120.9210.42895.8
3.09-3.173.30.1964.3714394384360.9840.23499.5
3.17-3.263.3930.1854.913744124050.9870.2298.3
3.26-3.363.4460.1296.6213924064040.9920.15499.5
3.36-3.473.3170.1796.0812673883820.9810.21498.5
3.47-3.63.3270.1088.0513544124070.9930.1398.8
3.6-3.733.1910.1018.8810883513410.9940.12297.2
3.73-3.883.2350.0859.5811423573530.9970.10398.9
3.88-4.062.8990.08410.579773503370.9930.10196.3
4.06-4.253.330.07413.3110593223180.9940.08798.8
4.25-4.483.5490.06516.6111253213170.9950.07798.8
4.48-4.763.480.06217.1810513073020.9950.07498.4
4.76-5.093.5230.05619.179302642640.9960.066100
5.09-5.493.3990.04822.429212732710.9930.05899.3
5.49-6.023.4350.04222.748212412390.9960.0599.2
6.02-6.733.4260.04222.247642262230.9980.0598.7
6.73-7.773.2140.03725.476171921920.9960.045100
7.77-9.513.0810.03725.695301721720.9970.045100
9.51-13.453.0380.0329.034011341320.9980.03798.5
13.45-48.0132.2470.03125.8418285810.9990.03895.3

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Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.008→48.013 Å / FOM work R set: 0.8176 / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.199 568 9.55 %
Rwork0.193 5381 -
obs-5949 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.05 Å2 / Biso mean: 59.13 Å2 / Biso min: 33.05 Å2
Refinement stepCycle: final / Resolution: 3.008→48.013 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1864 136 25 2025
Biso mean--56.52 50.19 -
Num. residues----88
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182224
X-RAY DIFFRACTIONf_angle_d1.3483456
X-RAY DIFFRACTIONf_chiral_restr0.667496
X-RAY DIFFRACTIONf_plane_restr0.0288
X-RAY DIFFRACTIONf_dihedral_angle_d15.71044
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0085-3.31120.27751390.26491298143797
3.3112-3.79010.21851470.20331302144997
3.7901-4.77450.19851390.18051366150598
4.7745-48.01940.16681430.17191415155899

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