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- PDB-4nya: Crystal structure of the E. coli thiM riboswitch in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4nya
TitleCrystal structure of the E. coli thiM riboswitch in complex with 5-(azidomethyl)-2-methylpyrimidin-4-amine
ComponentsthiM TPP riboswitch
KeywordsRNA / fragment-based drug discovery / riboswitch
Function / homology5-(azidomethyl)-2-methylpyrimidin-4-amine / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsWarner, K.D. / Homan, P. / Weeks, K.M. / Smith, A.G. / Abell, C. / Ferre-D'Amare, A.R.
CitationJournal: Chem.Biol. / Year: 2014
Title: Validating Fragment-Based Drug Discovery for Biological RNAs: Lead Fragments Bind and Remodel the TPP Riboswitch Specifically.
Authors: Warner, K.D. / Homan, P. / Weeks, K.M. / Smith, A.G. / Abell, C. / Ferre-D'Amare, A.R.
History
DepositionDec 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 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_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_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: thiM TPP riboswitch
B: thiM TPP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,77719
Polymers52,0842
Non-polymers69317
Water543
1
A: thiM TPP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,42511
Polymers26,0421
Non-polymers38310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: thiM TPP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3528
Polymers26,0421
Non-polymers3107
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.730, 29.890, 95.430
Angle α, β, γ (deg.)90.00, 93.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain thiM TPP riboswitch


Mass: 26042.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-2QB / 5-(azidomethyl)-2-methylpyrimidin-4-amine


Mass: 164.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 30% PEG4000, 0.1 M sodium acetate, pH 5.1, 0.3 M ammonium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2012
RadiationMonochromator: cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. obs: 11991 / % possible obs: 93.3 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.145 / Χ2: 2.162 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.65-2.72.90.5715770.816190.2
2.7-2.742.80.5066161.018194.8
2.74-2.82.90.5035661.004194
2.8-2.8530.4875931.031195.5
2.85-2.922.80.4036181.197196.1
2.92-2.982.90.355951.427194.3
2.98-3.063.30.3316231.696198.1
3.06-3.143.30.36201.841197.9
3.14-3.233.30.2615982.017194.8
3.23-3.343.40.256102.223193.1
3.34-3.463.40.2535682.178193
3.46-3.63.30.2355892.331192.2
3.6-3.763.30.2226012.133191.8
3.76-3.963.60.2096022.25195.1
3.96-4.23.60.1675962.408192.7
4.2-4.533.70.1515872.498191.1
4.53-4.983.40.1325942.794189.6
4.98-5.73.60.1096023.119193.9
5.7-7.163.50.1066033.408189.7
7.16-303.20.0846334.272189.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GDI

2gdi


Resolution: 2.65→30 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.273 1193 9.3 %
Rwork0.2251 10306 -
obs-11499 90 %
Solvent computationBsol: 26.6291 Å2
Displacement parametersBiso max: 107.67 Å2 / Biso mean: 62.5396 Å2 / Biso min: 28.05 Å2
Baniso -1Baniso -2Baniso -3
1--7.392 Å20 Å2-6.257 Å2
2--13.366 Å20 Å2
3----5.973 Å2
Refinement stepCycle: LAST / Resolution: 2.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3410 39 3 3452
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_scbond_it1.5632
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scangle_it2.5242.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2cycp-dna-rna_rep-13.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CCC.param
X-RAY DIFFRACTION6azmpDRGCNS.PAR
X-RAY DIFFRACTION7gtp.param

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