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- PDB-4mgn: Co-crystal structure of the G. kaustophilus glyQS T box riboswitc... -

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Basic information

Entry
Database: PDB / ID: 4mgn
TitleCo-crystal structure of the G. kaustophilus glyQS T box riboswitch Stem I in complex with tRNA
Components
  • glyQS T box riboswitch
  • tRNA-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 1.2Sep 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.pdbx_leaving_atom_flag / _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_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: glyQS T box riboswitch
B: tRNA-glycine
C: glyQS T box riboswitch
D: tRNA-glycine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,18522
Polymers104,7484
Non-polymers43718
Water00
1
A: glyQS T box riboswitch
B: tRNA-glycine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,59311
Polymers52,3742
Non-polymers2199
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-71 kcal/mol
Surface area25370 Å2
MethodPISA
2
C: glyQS T box riboswitch
D: tRNA-glycine
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,59311
Polymers52,3742
Non-polymers2199
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-72 kcal/mol
Surface area25880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.838, 205.182, 161.421
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain C
12chain D

NCS domain segments:

Dom-ID: 1 / Component-ID: 1 / Beg auth comp-ID: GTP / Beg label comp-ID: GTP / End auth comp-ID: C / End label comp-ID: C

Ens-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1chain 'C'CC10 - 951 - 86
2chain 'D'DD1 - 731 - 73

NCS ensembles :
ID
1
2

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Components

#1: RNA chain glyQS T box riboswitch


Mass: 28041.578 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: in vitro transcribed. Occurs naturally in Geobacillus kaustophilus
#2: RNA chain tRNA-glycine


Mass: 24332.295 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: in vitro transcribed. Occurs naturally in Geobacillus kaustophilus
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 18 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.67 Å3/Da / Density % sol: 66.48 %
Crystal growTemperature: 291 K / Method: hanging drop / pH: 7
Details: 80mM NaCl, 20mM MgCl2, 40mM sodium cacodylate, 12mM spermine, 10% 2-methyl-1,3 propanediol, pH 7.0, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2013
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce monochromator.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 26207 / % possible obs: 98.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 74.54 Å2 / Rmerge(I) obs: 0.16 / Χ2: 2.093 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allΧ2% possible allRmerge(I) obs
3.2-3.266.12.2912891.80496.9
3.26-3.316.63.112511.77698.4
3.31-3.386.63.4212921.86997.7
3.38-3.456.72.8212981.83998.6
3.45-3.526.83.1812611.82997.4
3.52-3.66.82.612831.81498
3.6-3.696.83.2312761.93898.4
3.69-3.796.83.6313162.12698.4
3.79-3.916.83.7812771.95498.40.978
3.91-4.036.93.7112972.0799.1
4.03-4.186.84.3513112.004990.875
4.18-4.346.94.5913022.06399.40.752
4.34-4.546.95.7913172.06699.40.6
4.54-4.7876.3413262.02999.50.546
4.78-5.087.28.7713162.09799.80.39
5.08-5.477.312.8113392.22599.90.261
5.47-6.027.415.7113412.3671000.215
6.02-6.897.318.5913352.4361000.181
6.89-8.677.129.5913702.4561000.104
8.67-50756.7814102.897.70.05

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4JRC and 4MGM

4jrc

4mgm


Resolution: 3.2→43.292 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.711 / SU ML: 0.45 / σ(F): 1.33 / Phase error: 34.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2783 2512 9.94 %
Rwork0.2364 --
obs0.2406 25268 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 294.72 Å2 / Biso mean: 141.6037 Å2 / Biso min: 38.12 Å2
Refinement stepCycle: LAST / Resolution: 3.2→43.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 6832 18 0 6850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0017636
X-RAY DIFFRACTIONf_angle_d0.45811904
X-RAY DIFFRACTIONf_chiral_restr0.0191581
X-RAY DIFFRACTIONf_plane_restr0.002317
X-RAY DIFFRACTIONf_dihedral_angle_d11.9513800
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C2026X-RAY DIFFRACTIONPOSITIONAL10.386
21D1658X-RAY DIFFRACTIONPOSITIONAL10.386
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2001-3.26160.36081340.3421176131094
3.2616-3.32810.37191360.34021213134994
3.3281-3.40050.34371350.34131205134096
3.4005-3.47960.34431320.33471195132795
3.4796-3.56650.36211380.33131243138197
3.5665-3.66290.36021350.3211244137997
3.6629-3.77060.35811410.30571250139198
3.7706-3.89230.3251380.26591264140298
3.8923-4.03130.30281340.26641268140299
4.0313-4.19260.33821340.2751258139299
4.1926-4.38320.35191390.26871283142299
4.3832-4.6140.30991370.25731276141399
4.614-4.90280.28221480.24812891437100
4.9028-5.28070.23211430.214412811424100
5.2807-5.8110.27441420.202513131455100
5.811-6.64920.24941460.222913171463100
6.6492-8.36740.22911470.208513211468100
8.3674-43.29590.21781530.17061360151398

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