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- PDB-4mgm: Crystal structure of the in vitro transcribed G. kaustophilus tRNA-Gly -

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Basic information

Entry
Database: PDB / ID: 4mgm
TitleCrystal structure of the in vitro transcribed G. kaustophilus tRNA-Gly
ComponentstRNA glycine
KeywordsRNA / RNA-RNA complex / base stacking / T-loop / RNA binding
Function / homologyRNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGrigg, J.C. / Ke, A.
CitationJournal: Structure / Year: 2013
Title: Structural Determinants for Geometry and Information Decoding of tRNA by T Box Leader RNA.
Authors: Grigg, J.C. / Ke, A.
History
DepositionAug 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: tRNA glycine
B: tRNA glycine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,68516
Polymers48,3452
Non-polymers34014
Water0
1
A: tRNA glycine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2946
Polymers24,1721
Non-polymers1225
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: tRNA glycine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,39110
Polymers24,1721
Non-polymers2199
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)161.233, 28.409, 132.939
Angle α, β, γ (deg.)90.00, 110.69, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain B) / NCS domain segments: (Selection details: chain 'B')

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Components

#1: RNA chain tRNA glycine


Mass: 24172.336 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: in vitro transcribed. Occurs naturally in Geobacillus kaustophilus
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg

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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: 2.95 Å3/Da / Density % sol: 58.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 75mM NaCl, 2mM CoCl2, 50mM sodium cacodylate, 0.5mM spermine, 30% w/v 1,6-Hexanediol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 1, 2012
RadiationMonochromator: Horizontal focusing 5.05 asymmetric cut Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 3.2→35 Å / Num. obs: 8419 / % possible obs: 82.8 % / Redundancy: 5.6 % / Biso Wilson estimate: 62.12 Å2 / Rmerge(I) obs: 0.158 / Net I/σ(I): 5.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.2-3.2640.3243.14146.2
3.26-3.314.10.2374.04151.7
3.31-3.383.90.2617.1153.2
3.38-3.454.10.2314.39153
3.45-3.523.90.3213.1160.5
3.52-3.64.20.2115.35165
3.6-3.694.20.3053.23170.7
3.69-3.794.10.2853.57181
3.79-3.94.80.2924185
3.9-4.035.20.3516.05191.2
4.03-4.175.20.3653.75195.4
4.17-4.345.70.3913.78196.7
4.34-4.546.20.335.08198.6
4.54-4.786.50.2397.58199.2
4.78-5.086.60.2049.25199.8
5.08-5.476.80.16311.181100
5.47-6.0170.142131100
6.01-6.8870.11114.21100
6.88-8.646.90.07519.361100
8.64-356.30.06324.7199.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.11data extraction
Adxvdata processing
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L0U

3l0u


Resolution: 3.2→33.169 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / σ(F): 1.34 / Phase error: 37.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2614 380 4.97 %
Rwork0.2477 --
obs0.2485 7647 77.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 98.3276 Å2
Refinement stepCycle: LAST / Resolution: 3.2→33.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2694 14 0 2708
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0013004
X-RAY DIFFRACTIONf_angle_d0.4034674
X-RAY DIFFRACTIONf_dihedral_angle_d13.2521494
X-RAY DIFFRACTIONf_chiral_restr0.02630
X-RAY DIFFRACTIONf_plane_restr0.002126
Refine LS restraints NCSNumber: 1384 / Type: POSITIONAL / Rms dev position: 5.757 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2004-3.6630.2513750.22151372X-RAY DIFFRACTION45
3.663-4.6130.31581360.25872688X-RAY DIFFRACTION87
4.613-33.17080.24261690.24823207X-RAY DIFFRACTION100

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