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- PDB-2oe8: 1.8 A X-ray crystal structure of Apramycin complex with RNA fragm... -

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Basic information

Entry
Database: PDB / ID: 2oe8
Title1.8 A X-ray crystal structure of Apramycin complex with RNA fragment GGGCGUCGCUAGUACC/CGGUACUAAAAGUCGCC containing the human ribosomal decoding A site: RNA construct with 5'-overhang
Components
  • RNA (5'-R(*CP*GP*GP*UP*AP*CP*UP*AP*AP*AP*AP*GP*UP*CP*GP*CP*C)-3')
  • RNA (5'-R(*GP*GP*GP*CP*GP*UP*CP*GP*CP*UP*AP*GP*UP*AP*CP*C)-3')
KeywordsRNA / Aminoglycoside antibiotics / Apramycin / Ribosomal decoding site / A site / Homo sapiens / RNA duplex
Function / homologyAPRAMYCIN / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHermann, T. / Tereshko, V. / Skripkin, E. / Patel, D.J.
CitationJournal: Blood Cells Mol.Dis. / Year: 2007
Title: Apramycin recognition by the human ribosomal decoding site.
Authors: Hermann, T. / Tereshko, V. / Skripkin, E. / Patel, D.J.
History
DepositionDec 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 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 / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE RESIDUES THAT ARE NATURALLY OCCURING IN THE HUMAN RIBOSOMAL DECODING A SITE ARE ...SEQUENCE THE RESIDUES THAT ARE NATURALLY OCCURING IN THE HUMAN RIBOSOMAL DECODING A SITE ARE NUMBERED 1404-1413 (CHAIN A) AND 1487-1497 (CHAIN B). THIS NUMBERING IS ADAPTED FROM THE BACTERIAL ESCHERICHIA COLI SEQUENCE. IN BOTH STRANDS TERMINAL RESIDUES ARE DISTINCT FROM HUMAN AND WERE INCORPORATED FOR CRYSTALLIZATION PURPOSES. THE INCORPORATED RESIDUES ARE NUMBERED 1-3, 14-16 (CHAIN A) AND 83-86,98-99 (CHAIN B)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,0953
Polymers10,5552
Non-polymers5401
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.858, 37.259, 85.586
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(*GP*GP*GP*CP*GP*UP*CP*GP*CP*UP*AP*GP*UP*AP*CP*C)-3')


Mass: 5129.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized
#2: RNA chain RNA (5'-R(*CP*GP*GP*UP*AP*CP*UP*AP*AP*AP*AP*GP*UP*CP*GP*CP*C)-3')


Mass: 5426.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized
#3: 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.: 1 / Source method: obtained synthetically / Formula: C21H41N5O11 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.1 Å3/Da / Density % sol: 41.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.05M MES BUFFER, 15-20% MPD, 0.02-0.04M MAGNESIUM ACETATE, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 5.6
Components of the solutions
IDNameCrystal-IDSol-ID
1MES BUFFER11
2MPD11
3MAGNESIUM ACETATE11
4MPD12
5MAGNESIUM ACETATE12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 8704 / Num. obs: 8704 / % possible obs: 99.44 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OE5

2oe5


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.144 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23611 440 5.1 %RANDOM
Rwork0.20836 ---
obs0.20984 8264 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.678 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å20 Å20 Å2
2--2.83 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 698 37 151 886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021819
X-RAY DIFFRACTIONr_bond_other_d0.0050.02297
X-RAY DIFFRACTIONr_angle_refined_deg1.81731271
X-RAY DIFFRACTIONr_angle_other_deg1.9093779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.6230.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02344
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021
X-RAY DIFFRACTIONr_nbd_refined0.1120.3101
X-RAY DIFFRACTIONr_nbd_other0.220.3379
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.5104
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.050.54
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0980.313
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1870.320
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.57
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it1.8553819
X-RAY DIFFRACTIONr_scangle_it2.5464.51271
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.437 33
Rwork0.291 594
Refinement TLS params.Method: refined / Origin x: 18.2279 Å / Origin y: -1.6955 Å / Origin z: 42.5781 Å
111213212223313233
T0.0478 Å2-0.0066 Å20.0149 Å2-0.03 Å20.0378 Å2--0.059 Å2
L1.3675 °20.2336 °2-0.3485 °2-0.1925 °2-0.0368 °2--0.9271 °2
S0.0887 Å °0.0215 Å °0.1746 Å °0.0198 Å °-0.0517 Å °0.0345 Å °-0.0749 Å °0.0344 Å °-0.037 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 31 - 3
2X-RAY DIFFRACTION1AA1404 - 14134 - 13
3X-RAY DIFFRACTION1AA14 - 1614 - 16
4X-RAY DIFFRACTION1BB83 - 861 - 4
5X-RAY DIFFRACTION1BB1487 - 14975 - 15
6X-RAY DIFFRACTION1BB98 - 9916 - 17
7X-RAY DIFFRACTION1BC - E101 - 252

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