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- PDB-5z71: Crystal structure of the Homo Sapiens cytoplasmic ribosomal decod... -

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Basic information

Entry
Database: PDB / ID: 5z71
TitleCrystal structure of the Homo Sapiens cytoplasmic ribosomal decoding site in complex with G418 (P21212 form)
ComponentsRNA (5'-R(P*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 / Resolution: 2.5 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
DepositionJan 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 30, 2019Provider: 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

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Assembly

Deposited unit
A: RNA (5'-R(P*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(P*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)14,5953
Polymers14,0982
Non-polymers4971
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-30 kcal/mol
Surface area7910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.924, 90.106, 46.701
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: RNA chain RNA (5'-R(P*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.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-GET / GENETICIN / G418


Mass: 496.552 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H40N4O10 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.31 Å3/Da / Density % sol: 46.7 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: MPD, Sodium chloride, Sprimine 4HCl, Sodium cacodylate (pH 5.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→45.053 Å / Num. obs: 8669 / % possible obs: 98.9 % / Redundancy: 3.827 % / Biso Wilson estimate: 65.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.029 / Rrim(I) all: 0.034 / Χ2: 1.087 / Net I/σ(I): 25.53
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.5-2.563.730.3133.616480.9090.36497.9
2.56-2.633.9550.2335.225970.960.26998.2
2.63-2.713.9440.1956.256220.9670.226100
2.71-2.793.8170.1378.56110.9820.159100
2.79-2.883.9250.09611.775730.9930.11198.5
2.88-2.983.9120.06817.075430.9970.079100
2.98-3.13.7740.03923.45540.9990.04598.2
3.1-3.223.8480.03128.224930.9990.037100
3.22-3.373.8310.03232.625040.9990.038100
3.37-3.533.7680.02834.784820.9990.03399.2
3.53-3.723.8570.02636.324460.9990.031100
3.72-3.953.8030.02939.444220.9990.03499.1
3.95-4.223.820.02541.234000.9990.028100
4.22-4.563.7640.02544.033770.9990.02998.7
4.56-4.993.8250.02345.693380.9990.027100
4.99-5.583.7470.02446.533120.9990.02799.4
5.58-6.453.7090.02545.142680.9990.02999.3
6.45-7.93.6950.02146.62390.9990.02499.6
7.9-11.173.8160.0249.0217410.02398.9
11.17-45.0533.4240.02246.26660.9990.02666.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.24data extraction
RefinementResolution: 2.5→45.053 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 35.31
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.3051 936 10.81 %
Rwork0.2695 --
obs0.2731 8659 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.79 Å2 / Biso mean: 63.5 Å2 / Biso min: 41.3 Å2
Refinement stepCycle: final / Resolution: 2.5→45.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 872 34 4 910
Biso mean--59.85 61.2 -
Num. residues----41
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151006
X-RAY DIFFRACTIONf_angle_d1.4871560
X-RAY DIFFRACTIONf_chiral_restr0.508220
X-RAY DIFFRACTIONf_plane_restr0.0241
X-RAY DIFFRACTIONf_dihedral_angle_d12.956484
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4966-2.62820.4521320.43891087121998
2.6282-2.79280.48541320.416711361268100
2.7928-3.00840.39241470.36241075122299
3.0084-3.31110.31961410.28431106124798
3.3111-3.790.25461370.251411121249100
3.79-4.77420.27381260.24081112123899
4.7742-45.06030.27971210.23451095121697

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