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- PDB-3td0: Crystal structure of the bacterial A1408G-mutant and the protozoa... -

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Basic information

Entry
Database: PDB / ID: 3td0
TitleCrystal structure of the bacterial A1408G-mutant and the protozoa cytoplasmic ribosomal decoding site
ComponentsRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
KeywordsRNA / Decoding / ribosome
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsKondo, J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2012
Title: A structural basis for the antibiotic resistance conferred by an A1408G mutation in 16S rRNA and for the antiprotozoal activity of aminoglycosides
Authors: Kondo, J.
History
DepositionAug 10, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*GP*(5BU)P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')
B: RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*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)15,0719
Polymers14,9012
Non-polymers1707
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-8 kcal/mol
Surface area8110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.520, 46.730, 55.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 7450.304 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Synthetic RNA
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sodium Cacodylate, Spermine tetrahydrochloride, Magnesium chloride, 2-methyl-2,4-pentanediol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SYNCHROTRONPhoton Factory BL-5A20.91921, 0.92100, 0.90615
Detector
TypeIDDetectorDate
ADSC QUANTUM 210r1CCDFeb 19, 2011
ADSC QUANTUM 210r2CCDDec 6, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Numerical link type Si(111) double crystal monochromator, direct water cooling using micro-channel (1st crystal), indirect water cooling (2nd crystal)SINGLE WAVELENGTHMx-ray1
2Numerical link type Si(111) double crystal monochromator, direct water cooling using micro-channel (1st crystal), indirect water cooling (2nd crystal)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.919211
30.9211
40.906151
ReflectionResolution: 1.6→35.7 Å / Num. obs: 16037 / % possible obs: 99.4 % / Redundancy: 7 % / Rmerge(I) obs: 0.049
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.235 / % possible all: 100

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Processing

Software
NameClassification
PHENIXmodel building
CNSrefinement
CrystalCleardata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→35.7 Å
RfactorNum. reflectionSelection details
Rfree0.256 -Random
Rwork0.22 --
obs-16031 -
Refinement stepCycle: LAST / Resolution: 1.6→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 939 7 199 1145
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.8

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