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- PDB-4p3s: Crystal structure of the bacterial A1408C-mutant ribosomal decodi... -

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Basic information

Entry
Database: PDB / ID: 4p3s
TitleCrystal structure of the bacterial A1408C-mutant ribosomal decoding site in complex with geneticin
Components5'-R(*UP*UP*GP*CP*GP*UP*CP*CP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'
KeywordsRNA/ANTIBIOTIC / ribosome / antibiotic-resistance / aminoglycoside / decoding / RNA-ANTIBIOTIC complex
Function / homologyGENETICIN / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsKondo, J. / Koganei, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
MEXT23790054 Japan
CitationJournal: To Be Published
Title: Crystal structure of the bacterial A1408C-mutant ribosomal decoding site in complex with geneticin
Authors: Kondo, J. / Koganei, M.
History
DepositionMar 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)16,3105
Polymers14,8212
Non-polymers1,4903
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-62 kcal/mol
Surface area8150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.090, 88.830, 46.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-226-

HOH

21A-266-

HOH

31B-124-

HOH

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Components

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


Mass: 7410.280 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-GET / GENETICIN / G418


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


Mass: 18.015 Da / Num. of mol.: 138 / 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: 2.41 Å3/Da / Density % sol: 48.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sodium Cacodylate (pH7), Spermine tetrahydrochloride, MPD, Sodium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.91938, 0.92004, 0.90659, 1.0
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 11, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.919381
20.920041
30.906591
411
ReflectionResolution: 2.3→44.42 Å / Num. obs: 6694 / % possible obs: 99.7 % / Redundancy: 6.72 % / Rmerge(I) obs: 0.05 / Χ2: 0.94 / Net I/σ(I): 17.6 / Num. measured all: 45316 / Scaling rejects: 340
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
2.3-2.387.040.3474.446636591.1821100
2.38-2.486.880.3244.444926511.110100
2.48-2.596.990.2276.246466601.0531100
2.59-2.736.760.1927.444526491.1863100
2.73-2.96.920.12310.345586570.9614100
2.9-3.126.890.07615.646696740.8623100
3.12-3.446.770.04623.745246630.853799.7
3.44-3.936.510.04226.844386700.777799.6
3.93-4.956.450.03830.344386870.7110100
4.95-44.426.050.02349.244367240.745497.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXphasing
CNSrefinement
PDB_EXTRACT3.14data extraction
SOLVEphasing
d*TREKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→100 Å / FOM work R set: 0.7962 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2646 726 10.8 %
Rwork0.2194 5968 -
obs-6694 99.6 %
Solvent computationBsol: 65.1243 Å2
Displacement parametersBiso max: 99.24 Å2 / Biso mean: 39.1932 Å2 / Biso min: 19.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.478 Å20 Å20 Å2
2--7.452 Å20 Å2
3----7.93 Å2
Refinement stepCycle: final / Resolution: 2.3→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 916 102 138 1156
Biso mean--45.54 46.94 -
Num. residues----43
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_scbond_it1.7172
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scangle_it2.4422.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.380.4083670.3967589656100
2.38-2.480.5019840.4463566650100
2.48-2.590.4026660.3508597663100
2.59-2.730.3122670.3121580647100
2.73-2.90.3791600.3008600660100
2.9-3.120.3026860.2213583669100
3.12-3.440.2478700.209959866899.7
3.44-3.930.2233770.182159367099.6
3.93-4.960.2207750.1545612687100
4.96-1000.2057740.190465072497.3
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1dna-rna_free.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4bru.param
X-RAY DIFFRACTION5get_xplor.param

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