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- PDB-3l0u: The crystal structure of unmodified tRNAPhe from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 3l0u
TitleThe crystal structure of unmodified tRNAPhe from Escherichia coli
ComponentsUnmodified tRNAPhe
KeywordsRNA / transfer RNA / tRNA / transcript / unmodified
Function / homology: / : / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsByrne, R.T. / Konevega, A.L. / Rodnina, M.V. / Antson, A.A.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: The crystal structure of unmodified tRNAPhe from Escherichia coli
Authors: Byrne, R.T. / Konevega, A.L. / Rodnina, M.V. / Antson, A.A.
History
DepositionDec 10, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Dec 25, 2019Group: Advisory / Data collection / Source and taxonomy
Category: pdbx_entity_src_syn / pdbx_unobs_or_zero_occ_residues / reflns_shell
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _reflns_shell.Rmerge_I_obs
Revision 1.4Nov 10, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / 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 / _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_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_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_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_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 1.5Nov 1, 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: Unmodified tRNAPhe
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5734
Polymers24,4861
Non-polymers883
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.450, 99.450, 110.330
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#1: RNA chain Unmodified tRNAPhe


Mass: 24485.539 Da / Num. of mol.: 1 / Mutation: C3G, G70C / Source method: obtained synthetically / Details: In vitro synthesis by T7 RNA polymerase / Source: (synth.) Escherichia coli K12 (bacteria) / References: GenBank: CP001637.1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.22 Å3/Da / Density % sol: 61.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.3M KCL, 0.1M Hepes pH 7.5, 35% v/v MPD, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9704 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2009
Details: Kirkpatrick Baez bimorph mirror pair for horizontal and vertical focussing.
RadiationMonochromator: Double crystal Si(111). / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9704 Å / Relative weight: 1
ReflectionResolution: 3→46.45 Å / Num. obs: 6886 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.7 % / Biso Wilson estimate: 70.9 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 12.3
Reflection shellResolution: 3→3.16 Å / Redundancy: 16.4 % / Rmerge(I) obs: 1.244 / Mean I/σ(I) obs: 2.3 / Num. unique all: 971 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.5.0088refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EHZ

1ehz


Resolution: 3→40.12 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.887 / Occupancy max: 1 / Occupancy min: 0 / SU B: 35.836 / SU ML: 0.305 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.678 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. B VALUES ARE TOTAL B VALUES (THE SUM OF THE RESIDUAL AND TLS CONTRIBUTIONS).
RfactorNum. reflection% reflectionSelection details
Rfree0.261 312 4.5 %RANDOM
Rwork0.226 ---
obs0.228 6865 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 144.84 Å2 / Biso mean: 88.217 Å2 / Biso min: 27.96 Å2
Refinement stepCycle: LAST / Resolution: 3→40.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1561 3 9 1573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0211749
X-RAY DIFFRACTIONr_bond_other_d0.0010.02601
X-RAY DIFFRACTIONr_angle_refined_deg0.76132729
X-RAY DIFFRACTIONr_angle_other_deg0.69631566
X-RAY DIFFRACTIONr_chiral_restr0.050.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02757
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02162
X-RAY DIFFRACTIONr_scbond_it0.25931749
X-RAY DIFFRACTIONr_scangle_it0.4474.52729
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 15 -
Rwork0.312 475 -
all-490 -
obs--99.8 %
Refinement TLS params.Method: refined / Origin x: 14.0525 Å / Origin y: -26.7749 Å / Origin z: 3.7635 Å
111213212223313233
T0.1125 Å2-0.0128 Å2-0.0029 Å2-0.0891 Å2-0.0749 Å2--0.211 Å2
L3.9977 °22.619 °2-0.9371 °2-2.6517 °2-0.6019 °2--1.7031 °2
S-0.288 Å °0.0895 Å °-0.7238 Å °-0.4218 Å °0.1432 Å °-0.3761 Å °0.1063 Å °-0.0835 Å °0.1448 Å °

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