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- PDB-5z1i: Crystal structure of the protozoal cytoplasmic ribosomal decoding... -

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Basic information

Entry
Database: PDB / ID: 5z1i
TitleCrystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-fluoro sisomicin
ComponentsRNA (5'-R(P*GP*CP*GP*UP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
KeywordsRNA / rRNA / aminoglycoside
Function / homologyChem-FSJ / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.903 Å
AuthorsKanazawa, H. / Hanessian, S. / Kondo, J.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)17K08248 Japan
CitationJournal: ChemMedChem / Year: 2018
Title: Structure-Based Design of a Eukaryote-Selective Antiprotozoal Fluorinated Aminoglycoside.
Authors: Kanazawa, H. / Saavedra, O.M. / Maianti, J.P. / Young, S.A. / Izquierdo, L. / Smith, T.K. / Hanessian, S. / Kondo, J.
History
DepositionDec 26, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 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*GP*CP*GP*UP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2252
Polymers6,7741
Non-polymers4511
Water1,31573
1
A: RNA (5'-R(P*GP*CP*GP*UP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
hetero molecules

A: RNA (5'-R(P*GP*CP*GP*UP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4494
Polymers13,5482
Non-polymers9012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area2530 Å2
ΔGint-19 kcal/mol
Surface area8100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.171, 46.171, 115.294
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-457-

HOH

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Components

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


Mass: 6774.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-FSJ / (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(fluoromethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside / 6'-fluoro sisomicin


Mass: 450.502 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C19H35FN4O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2-Methyl-2,4-pentanediol, LiCl, spermine tetrahydrochloride, sodium cacodylate

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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: Mar 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→42.862 Å / Num. obs: 5236 / % possible obs: 99.8 % / Redundancy: 11.955 % / Biso Wilson estimate: 20.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.075 / Χ2: 1.044 / Net I/σ(I): 23.85
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.9511.4810.2757.863740.9870.28899.2
1.95-2.0112.350.2828.933710.9810.294100
2.01-2.0612.2170.23110.293500.9920.241100
2.06-2.1312.6290.18613.483340.9930.194100
2.13-2.212.7840.17314.133480.9950.18100
2.2-2.2712.830.16914.783170.9960.176100
2.27-2.3612.5410.14517.673160.9960.151100
2.36-2.4612.0550.11620.423090.9960.121100
2.46-2.5712.140.11420.992990.9970.119100
2.57-2.6912.0990.10124.782720.9970.106100
2.69-2.8412.5780.08928.482750.9950.093100
2.84-3.0112.3480.07532.62530.9980.07899.6
3.01-3.2211.7690.0638.862380.9990.06399.6
3.22-3.4710.760.05539.952290.9990.05898.7
3.47-3.8110.8550.05141.332070.9990.05499.5
3.81-4.2610.8320.04544.641960.9990.04799.5
4.26-4.9111.6030.04246.841740.9990.04499.4
4.91-6.0210.9610.03843.291550.9990.04100
6.02-8.519.9590.03343.21230.9990.035100
8.51-42.8629.4270.0345.26820.9990.03297.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.24data extraction
RefinementResolution: 1.903→42.862 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.82
RfactorNum. reflection% reflection
Rfree0.224 544 10.59 %
Rwork0.196 --
obs-5223 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 198.25 Å2 / Biso mean: 25.48 Å2 / Biso min: 12.5 Å2
Refinement stepCycle: final / Resolution: 1.903→42.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 451 31 73 555
Biso mean--20.09 32.42 -
Num. residues----21
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006536
X-RAY DIFFRACTIONf_angle_d1.02832
X-RAY DIFFRACTIONf_chiral_restr0.105116
X-RAY DIFFRACTIONf_plane_restr0.01421
X-RAY DIFFRACTIONf_dihedral_angle_d11.877251
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 (%)
1.9032-2.00350.26061380.22751189132799
2.0035-2.1290.2341590.212111581317100
2.129-2.29340.20931260.209612141340100
2.2934-2.52420.2431600.209711891349100
2.5242-2.88940.26741400.235112041344100
2.8894-3.640.18791420.19711176131899
3.64-42.87270.16521240.143312241348100

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