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- PDB-4p3u: Crystal structure of the bacterial A1408U-mutant ribosomal decodi... -

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Basic information

Entry
Database: PDB / ID: 4p3u
TitleCrystal structure of the bacterial A1408U-mutant ribosomal decoding site (C2 form 1)
Components5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'
KeywordsRNA / ribosome / antibiotic-resistance / aminoglycoside / decoding
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsKondo, J. / Koganei, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
MEXT23790054 Japan
CitationJournal: To Be Published
Title: Crystal structure of the bacterial A1408U-mutant ribosomal decoding site (C2 form 1)
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*UP*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*UP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'
C: 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'
D: 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)29,6454
Polymers29,6454
Non-polymers00
Water25214
1
A: 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*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*UP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)14,8232
Polymers14,8232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-16 kcal/mol
Surface area8440 Å2
MethodPISA
2
C: 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'
D: 5'-R(*UP*UP*GP*CP*GP*UP*CP*UP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)14,8232
Polymers14,8232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-18 kcal/mol
Surface area8450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.380, 32.730, 80.990
Angle α, β, γ (deg.)90.000, 117.060, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 7411.264 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.13 Å3/Da / Density % sol: 60.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sodium Cacodylate, Spermine tetrahydrochloride, PEG3350, 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 315r / Detector: CCD / Date: Feb 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3→25.6 Å / Num. obs: 7533 / % possible obs: 99.4 % / Redundancy: 3.53 % / Rmerge(I) obs: 0.091 / Χ2: 0.98 / Net I/σ(I): 7.1 / Num. measured all: 26787 / Scaling rejects: 201
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
3-3.113.570.3772.226357291.1333100
3.11-3.233.590.2422.627327581.151399.9
3.23-3.383.590.1563.326877451.0613100
3.38-3.563.610.1813.426797391.06899.9
3.56-3.783.580.1264.326877460.941599.9
3.78-4.073.560.1115.727157560.962099.9
4.07-4.483.530.106726857550.921799.9
4.48-5.123.540.0888.127187640.8415100
5.12-6.433.510.06911.827247710.811699.9
6.43-25.63.210.03724.325257700.985195.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CNSrefinement
PDB_EXTRACT3.14data extraction
MOLREPphasing
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→100 Å / FOM work R set: 0.6361 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.3024 808 10.6 %
Rwork0.2951 6724 -
obs-7532 99.2 %
Solvent computationBsol: 69.0349 Å2
Displacement parametersBiso max: 224.93 Å2 / Biso mean: 142.0724 Å2 / Biso min: 56.8 Å2
Baniso -1Baniso -2Baniso -3
1--23.491 Å20 Å254.464 Å2
2---1.739 Å20 Å2
3---25.231 Å2
Refinement stepCycle: final / Resolution: 3→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1832 0 14 1846
Biso mean---80.9 -
Num. residues----86
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.287
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_scbond_it1.2822
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scangle_it2.112.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.110.5907790.6207649X-RAY DIFFRACTION100
3.11-3.230.6184770.53687X-RAY DIFFRACTION99.9
3.23-3.380.5075800.4564662X-RAY DIFFRACTION100
3.56-3.780.3538790.4021662X-RAY DIFFRACTION99.9
3.78-4.070.369840.3543666X-RAY DIFFRACTION99.9
4.07-4.480.2625830.28671X-RAY DIFFRACTION99.9
4.48-5.130.2367780.2495677X-RAY DIFFRACTION99.9
5.13-6.460.2737890.2367675X-RAY DIFFRACTION99.9
6.46-25.60.2143770.1965702X-RAY DIFFRACTION99.9
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1bru.param
X-RAY DIFFRACTION2dna-rna_free.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

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