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- PDB-4p3t: Crystal structure of the bacterial A1408C-mutant ribosomal decodi... -

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Basic information

Entry
Database: PDB / ID: 4p3t
TitleCrystal structure of the bacterial A1408C-mutant ribosomal decoding site
Components5'-D(*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 / ribosome / antibiotic-resistance / aminoglycoside / decoding
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 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
Authors: Kondo, J. / Koganei, M.
History
DepositionMar 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.2Dec 27, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*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'-D(*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'


Theoretical massNumber of molelcules
Total (without water)14,8212
Polymers14,8212
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-17 kcal/mol
Surface area8500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.437, 40.475, 41.272
Angle α, β, γ (deg.)90.000, 103.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain 5'-D(*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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 1.86 Å3/Da / Density % sol: 33.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sodium Cacodylate (pH7), Spermine tetrahydrochloride, MPD, Ammonium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.91992, 0.92005, 0.90660, 1.0
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 30, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.919921
20.920051
30.90661
411
ReflectionResolution: 1.6→40.2 Å / Num. obs: 14089 / % possible obs: 98.4 % / Redundancy: 7.21 % / Rmerge(I) obs: 0.039 / Χ2: 0.95 / Net I/σ(I): 19.2 / Num. measured all: 102374 / Scaling rejects: 768
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.6-1.667.230.2954.91026314061.2799100
1.66-1.727.280.2026.21047914301.1370100
1.72-1.87.280.177.71045114251.0477100
1.8-1.97.340.14391043114110.967999.9
1.9-2.027.380.10511.51059814280.8759100
2.02-2.177.370.07815.11064814370.8461100
2.17-2.397.390.06418.91065314330.847099.9
2.39-2.747.410.04281061514210.8184100
2.74-3.457.170.02644.41013114050.786097.4
3.45-40.26.180.02655.5810512930.9910987.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
CNSrefinement
PDB_EXTRACT3.14data extraction
SOLVEphasing
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.6→20 Å / FOM work R set: 0.7783 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2706 1430 10 %
Rwork0.2477 12655 -
obs-14085 98.4 %
Solvent computationBsol: 57.6509 Å2
Displacement parametersBiso max: 66.58 Å2 / Biso mean: 35.855 Å2 / Biso min: 14.27 Å2
Baniso -1Baniso -2Baniso -3
1--1.081 Å20 Å23.317 Å2
2---0.598 Å20 Å2
3---1.679 Å2
Refinement stepCycle: final / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 970 0 150 1120
Biso mean---42.03 -
Num. residues----46
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_d0.881
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_scbond_it1.472
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scangle_it2.1022.5
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 (%)
1.6-1.660.3681410.317312651406100
1.66-1.720.3621310.303112961427100
1.72-1.80.33771350.297812841419100
1.8-1.90.35171550.30251264141999.9
1.9-2.020.33691420.289212791421100
2.02-2.170.29551290.251213041433100
2.17-2.390.29251780.27081257143599.9
2.39-2.730.28791420.264112781420100
2.73-3.440.26641560.24321257141397.4
3.44-200.20691210.20431171129287.7
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

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