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- PDB-1i9v: CRYSTAL STRUCTURE ANALYSIS OF A TRNA-NEOMYCIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1i9v
TitleCRYSTAL STRUCTURE ANALYSIS OF A TRNA-NEOMYCIN COMPLEX
ComponentsPHENYLALANINE TRANSFER RNA
KeywordsRNA / AMINO-ACID TRANSPORT / YEAST / PHE-TRNA / PHENYLALANINE / TRANSFER RNA / AMINOGLYCOSIDE / NEOMYCIN B
Function / homologyNEOMYCIN / : / RNA / RNA (> 10)
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMikkelsen, N.E. / Johansson, K. / Virtanen, A. / Kirsebom, L.A.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Aminoglycoside binding displaces a divalent metal ion in a tRNA-neomycin B complex.
Authors: Mikkelsen, N.E. / Johansson, K. / Virtanen, A. / Kirsebom, L.A.
History
DepositionMar 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHENYLALANINE TRANSFER RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4455
Polymers24,7581
Non-polymers6884
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.900, 32.900, 63.100
Angle α, β, γ (deg.)90.00, 90.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain PHENYLALANINE TRANSFER RNA


Mass: 24757.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: GenBank: 176479
#2: Chemical ChemComp-NMY / NEOMYCIN / MYCIFRADIN / NEOMAS / PIMAVECORT / VONAMYCIN


Mass: 614.644 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H46N6O13 / Comment: antibiotic*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6
Details: MgCl, MPD, Cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 281K
Components of the solutions
IDNameCrystal-IDSol-ID
1MgCl11
2MPD11
3Cacodylate11
4MPD12
Crystal grow
*PLUS
Temperature: 6 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 %MPD1reservoir
280 mMsodium cacodylate1reservoir
340 mM1reservoirMgCl2
425 mg/mlprotein1drop
52 mM1dropMgCl2
610 mMneomycin B1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.104 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 25, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.104 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 6515 / Num. obs: 6515 / % possible obs: 90.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 1.6 % / Biso Wilson estimate: 69.98 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.3
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.65 Å / % possible obs: 76 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 6TNA

6tna


Resolution: 2.6→20 Å / Isotropic thermal model: isotropic / σ(F): 0 / σ(I): 0
Stereochemistry target values: Parkinson, Vojtechovsky, Clowney, Brunger, Berman, New Parameters for the Refinement of Nucleic Acid Containing Structures, Acta Cryst. D, 52, 57-64 (1996).
RfactorNum. reflection% reflectionSelection details
Rfree0.275 304 -RANDOM
Rwork0.228 ---
all0.2297 6515 --
obs0.2297 6515 90.8 %-
Displacement parametersBiso mean: 48 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1631 45 32 1708
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.39
X-RAY DIFFRACTIONc_bond_d0.0108
LS refinement shellResolution: 2.6→2.65 Å / % reflection obs: 75.9 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 48 Å2

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