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Basic information

Entry
Database: PDB / ID: 6jbg
TitleCrystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (equatorial 4'-F)
Components
  • RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
  • RNA (5'-R(P*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
KeywordsRNA/ANTIBIOTIC / RNA / antibiotic / RNA-ANTIBIOTIC complex
Function / homologyChem-S81 / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKanazawa, H. / Auffinger, P. / Hanessian, S. / Kondo, J.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)26860025 Japan
CitationJournal: To Be Published
Title: Crystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (axial 4'-F)
Authors: Kondo, J. / Hanessian, S. / Kanazawa, H.
History
DepositionJan 25, 2019Deposition site: PDBJ / Processing site: PDBJ
SupersessionJan 29, 2020ID: 5BXK
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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(P*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
B: RNA (5'-R(P*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
C: RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
D: RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*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)29,1945
Polymers28,8694
Non-polymers3241
Water46826
1
A: RNA (5'-R(P*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
B: RNA (5'-R(P*UP*GP*CP*GP*UP*CP*AP*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)14,4533
Polymers14,1292
Non-polymers3241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-11 kcal/mol
Surface area8280 Å2
MethodPISA
2
C: RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
D: RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)14,7412
Polymers14,7412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-15 kcal/mol
Surface area8410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.382, 83.720, 51.444
Angle α, β, γ (deg.)90.000, 95.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 7064.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')


Mass: 7370.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Sugar ChemComp-S81 / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-glucopyranoside / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-glucoside / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-D-glucoside / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-glucoside


Type: D-saccharide / Mass: 324.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H25FN4O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.11 Å3/Da / Density % sol: 41.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, KCl, Sodium cacodylate, Spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→43.704 Å / Num. obs: 4396 / % possible obs: 99.8 % / Redundancy: 6.69 % / Biso Wilson estimate: 49.67 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.128 / Rrim(I) all: 0.139 / Χ2: 1.001 / Net I/σ(I): 11.19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.1-3.186.790.3633.563330.9880.39397.7
3.18-3.276.7750.284.673020.9930.303100
3.27-3.366.5540.3094.852960.9920.336100
3.36-3.466.9070.2925.283010.9920.316100
3.46-3.586.7530.2695.483040.9930.29199.7
3.58-3.76.7330.2066.952620.9940.223100
3.7-3.846.4230.2087.192790.9930.226100
3.84-46.7960.1628.852690.9970.175100
4-4.186.7940.15511.372380.9940.16899.6
4.18-4.386.610.1611.872410.9940.173100
4.38-4.627.110.14612.932280.9910.15899.6
4.62-4.96.7590.12314.222120.9920.133100
4.9-5.246.4170.11715.471990.9930.128100
5.24-5.666.8770.08919.572040.9970.096100
5.66-6.26.3380.10316.831600.9940.11298.8
6.2-6.936.8980.07422.411660.9970.08100
6.93-86.3120.06324.881380.9960.069100
8-9.86.430.06224.021210.9990.067100
9.8-13.866.4950.04530.79910.9970.04998.9
13.86-43.7045.8460.04129.93520.9990.04598.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J7T

1j7t


Resolution: 3.1→43.704 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.81
RfactorNum. reflection% reflection
Rfree0.2253 418 9.66 %
Rwork0.1609 --
obs0.1667 4329 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 111.6 Å2 / Biso mean: 54.99 Å2 / Biso min: 20.5 Å2
Refinement stepCycle: final / Resolution: 3.1→43.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1914 22 26 1962
Biso mean--39.75 44.19 -
Num. residues----90
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012160
X-RAY DIFFRACTIONf_angle_d0.9533354
X-RAY DIFFRACTIONf_chiral_restr0.042458
X-RAY DIFFRACTIONf_plane_restr0.00594
X-RAY DIFFRACTIONf_dihedral_angle_d11.2791066
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.099-3.54730.28871300.21283141397
3.5473-4.46850.23811510.16011278142999
4.4685-43.70880.19461370.147313501487100

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