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- PDB-1yrj: Crystal Structure of Apramycin bound to a Ribosomal RNA A site ol... -

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Basic information

Entry
Database: PDB / ID: 1yrj
TitleCrystal Structure of Apramycin bound to a Ribosomal RNA A site oligonucleotide
ComponentsBacterial 16 S Ribosomal RNA A Site Oligonucleotide
KeywordsRNA / RNA complex / Apramycin-RNA Complex / Molecular Recognition
Function / homologyAPRAMYCIN / : / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.7 Å
AuthorsHan, Q. / Zhao, Q. / Fish, S. / Simonsen, K.B. / Vourloumis, D. / Froelich, J.M. / Wall, D. / Hermann, T.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2005
Title: Molecular recognition by glycoside pseudo base pairs and triples in an apramycin-RNA complex.
Authors: Han, Q. / Zhao, Q. / Fish, S. / Simonsen, K.B. / Vourloumis, D. / Froelich, J.M. / Wall, D. / Hermann, T.
History
DepositionFeb 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 30, 2016Group: Other
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: Bacterial 16 S Ribosomal RNA A Site Oligonucleotide
B: Bacterial 16 S Ribosomal RNA A Site Oligonucleotide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8536
Polymers14,7112
Non-polymers1,1434
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.250, 30.900, 45.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: RNA chain Bacterial 16 S Ribosomal RNA A Site Oligonucleotide


Mass: 7355.409 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-AM2 / APRAMYCIN / NEBRAMYCIN II / 4-O-(3ALPHA-AMINO-6ALPHA-((4-AMINO-4-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY)-2,3,4,5ABETA,6,7,8,8AALPHA-OCTAHYDRO-8BETA-HYDROXY-7BETA-(METHYLAMINO)PYRANO(3,2-B)PYRAN-2ALPHA-YL)-2-DEOXY-D-STREPTAMINE / Apramycin


Mass: 539.577 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H41N5O11 / Comment: antibiotic*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growTemperature: 310 K / Method: evaporation / pH: 6.5
Details: MPD, sodium cacodylate, NaCl, KCl, MgSO4, pH 6.5, EVAPORATION, temperature 310K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPD11
2sodium cacodylate11
3NaClSodium chloride11
4KCl11
5MgSO411
6H2O11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.127 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 30, 2004 / Details: mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2.7→8 Å / Num. obs: 3802 / % possible obs: 99 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 43
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.17 / % possible all: 99

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MIR
Starting model: PDB entry 1LC4

1lc4


Resolution: 2.7→8 Å / σ(F): 1.5 / σ(I): 1.5
RfactorNum. reflection% reflectionSelection details
Rfree0.307 -10 %RANDOM
Rwork0.246 ---
obs-3712 99 %-
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 952 76 65 1093
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.63

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