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- PDB-6jbf: Crystal structure of the bacterial ribosomal decoding site in com... -

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Basic information

Entry
Database: PDB / ID: 6jbf
TitleCrystal structure of the bacterial ribosomal decoding site in complex with 4'-deoxy-4'-fluoro neamine analog (axial 4'-F)
ComponentsRNA (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')
KeywordsRNA/ANTIBIOTIC / RNA / antibiotic / RNA-ANTIBIOTIC complex
Function / homologyChem-V71 / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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: 5BWS
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

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Assembly

Deposited unit
A: 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')
B: 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')
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)29,8065
Polymers29,4824
Non-polymers3241
Water1,71195
1
A: 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')
B: 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)15,0653
Polymers14,7412
Non-polymers3241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-14 kcal/mol
Surface area8230 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 area2080 Å2
ΔGint-18 kcal/mol
Surface area8340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.111, 81.324, 50.131
Angle α, β, γ (deg.)90.000, 95.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: 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.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Sugar ChemComp-V71 / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-galactopyranoside / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-galactoside / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-D-galactoside / (1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 2,6-diamino-2,4,6-trideoxy-4-fluoro-galactoside


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


Mass: 18.015 Da / Num. of mol.: 95 / 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 % sol: 34.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, NaCl, spermine tetrahydrochloride, sodium cacodylate

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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: 2.6→42.543 Å / Num. obs: 6744 / % possible obs: 99.8 % / Redundancy: 6.782 % / Biso Wilson estimate: 35.08 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.061 / Χ2: 0.993 / Net I/σ(I): 25.15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.6-2.666.850.2817.634930.9620.30598.6
2.66-2.746.6020.2448.154950.9760.265100
2.74-2.827.0330.19110.494590.9830.207100
2.82-2.97.0180.14313.434530.9950.15499.6
2.9-36.7760.1115.744550.9960.119100
3-3.16.8110.07220.664240.9990.078100
3.1-3.226.9030.06223.724110.9990.067100
3.22-3.356.6330.06423.414140.9990.069100
3.35-3.57.090.05526.873770.9990.0699.7
3.5-3.676.8320.05627.313580.9990.061100
3.67-3.876.4550.04729.693650.9990.05199.7
3.87-4.16.8640.04336.823090.9990.04799.7
4.1-4.396.5960.04138.333120.9980.04599.4
4.39-4.746.8680.04337.262880.9990.047100
4.74-5.196.5060.03842.372650.9990.042100
5.19-5.86.8440.03545.542440.9990.037100
5.8-6.76.7560.03442.882210.9990.037100
6.7-8.216.6270.03245.781770.9990.03498.9
8.21-11.616.5740.02845.8614110.03100
11.61-42.5436.1690.02252.128310.02498.8

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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: 2.6→42.543 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.94
RfactorNum. reflection% reflection
Rfree0.229 670 9.97 %
Rwork0.1538 --
obs0.1613 6718 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.41 Å2 / Biso mean: 32.58 Å2 / Biso min: 13.73 Å2
Refinement stepCycle: final / Resolution: 2.6→42.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1948 22 95 2065
Biso mean--23.3 30.02 -
Num. residues----92
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092197
X-RAY DIFFRACTIONf_angle_d1.0533414
X-RAY DIFFRACTIONf_chiral_restr0.044466
X-RAY DIFFRACTIONf_plane_restr0.00692
X-RAY DIFFRACTIONf_dihedral_angle_d9.8751088
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5954-2.79570.38221390.248912031342100
2.7957-3.0770.29721330.204512101343100
3.077-3.52210.24681400.16331184132499
3.5221-4.43670.18761290.12321216134599
4.4367-42.54850.16981290.12261235136499

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