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- PDB-1ntb: 2.9 A crystal structure of Streptomycin RNA-aptamer complex -

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Basic information

Entry
Database: PDB / ID: 1ntb
Title2.9 A crystal structure of Streptomycin RNA-aptamer complex
Components
  • 5'-R(*CP*GP*GP*CP*AP*CP*CP*AP*CP*GP*GP*UP*CP*GP*GP*AP*UP*C)-3'
  • 5'-R(*GP*GP*AP*UP*CP*GP*CP*AP*UP*UP*UP*GP*GP*AP*CP*UP*UP*CP*UP*GP*CP*C)-3'
KeywordsRNA / Streptomycin RNA-Aptamer / Magnesium form
Function / homologySTREPTOMYCIN / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTereshko, V. / Skripkin, E. / Patel, D.J.
CitationJournal: CHEM.BIOL. / Year: 2003
Title: Encapsulating Streptomycin within a small 40-mer RNA
Authors: Tereshko, V. / Skripkin, E. / Patel, D.J.
History
DepositionJan 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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_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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,4036
Polymers12,7512
Non-polymers6524
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.634, 82.634, 49.153
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

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RNA chain , 2 types, 2 molecules AB

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


Mass: 6988.146 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: RNA chain 5'-R(*CP*GP*GP*CP*AP*CP*CP*AP*CP*GP*GP*UP*CP*GP*GP*AP*UP*C)-3'


Mass: 5762.499 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 10 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SRY / STREPTOMYCIN / STREPTOMYCIN A / Streptomycin


Mass: 581.574 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H39N7O12 / Comment: medication, antibiotic*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.29 Å3/Da / Density % sol: 62.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: MES buffer, Magnesium cloride, sodium cloride, MPD, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MES buffer11
2MgCl211
3NaClSodium chloride11
4MPD11
5MgCl212
6NaClSodium chloride12
7MPD12
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.24 mMRNA1drop
217 mMMES1droppH5.6
312.5 mM1dropBaCl2
425 mM1dropMgCl2
565 mM1dropNaCl
66 %MPD1drop
717.5 %1reservoir
850 mMMES1reservoirpH5.6
925 mM1reservoirBaCl2
1075 mM1reservoirMgCl2
1165 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 24, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.85→25 Å / Num. obs: 3942 / % possible obs: 99.8 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.045
Reflection shellResolution: 2.85→2.95 Å / Rmerge(I) obs: 0.45 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 30 Å / Num. obs: 3774 / % possible obs: 99.9 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 100 % / Num. unique obs: 371 / Rmerge(I) obs: 0.32

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Processing

Software
NameVersionClassification
REFMAC5.1.13refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Barium form of streptomycin RNA-aptamer

Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 16.131 / SU ML: 0.299 / Cross valid method: THROUGHOUT / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25507 349 9.3 %RANDOM
Rwork0.20373 ---
obs0.20847 3394 99.84 %-
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: 45.528 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20 Å20 Å2
2--0.51 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 842 43 6 891
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021988
X-RAY DIFFRACTIONr_bond_other_d0.0020.02327
X-RAY DIFFRACTIONr_angle_refined_deg1.7462.1211525
X-RAY DIFFRACTIONr_angle_other_deg1.712.049854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.4120.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02418
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024
X-RAY DIFFRACTIONr_nbd_refined0.1790.2177
X-RAY DIFFRACTIONr_nbd_other0.2270.2407
X-RAY DIFFRACTIONr_nbtor_other0.110.2198
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.230
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.210
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it0.8533988
X-RAY DIFFRACTIONr_scangle_it1.3724.51525
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.359 22
Rwork0.3 234
Refinement TLS params.Method: refined / Origin x: 13.0915 Å / Origin y: 30.3084 Å / Origin z: 0.7858 Å
111213212223313233
T0.2346 Å20.2198 Å20.0239 Å2-0.2111 Å20.0065 Å2--0.3656 Å2
L4.4955 °20.2268 °2-0.557 °2-5.6035 °2-3.8731 °2--9.374 °2
S-0.4998 Å °0.3799 Å °-0.2448 Å °0.1511 Å °0.5065 Å °-0.3314 Å °0.0325 Å °-0.0659 Å °-0.0066 Å °
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.75
LS refinement shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å / Rfactor Rwork: 0.3

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