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

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Basic information

Entry
Database: PDB / ID: 4nyd
TitleCrystal structure of the E. coli thiM riboswitch in complex with hypoxanthine
ComponentsthiM TPP riboswitch
KeywordsRNA / fragment-based drug discovery / riboswitch
Function / homologyHYPOXANTHINE / : / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,36312
Polymers26,8611
Non-polymers50211
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.436, 65.436, 101.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: RNA chain thiM TPP riboswitch


Mass: 26860.900 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#2: Chemical ChemComp-HPA / HYPOXANTHINE / Hypoxanthine


Mass: 136.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N4O
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG2000, 0.5 M ammonium chloride, 50 mM succinate/KOH, pH 7.0, 10 mM manganese chloride, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2011
RadiationMonochromator: liquid nitrogen cooled dual crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 5634 / % possible obs: 99.4 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.077 / Χ2: 1.581 / Net I/σ(I): 15.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-2.952.70.5762781.032199.3
2.95-32.80.5842581.1199.2
3-3.062.80.4682911.0561100
3.06-3.1230.32791.0061100
3.12-3.1930.2262661.2671100
3.19-3.2730.1693011.207199.7
3.27-3.3530.1742601.41100
3.35-3.4430.1582991.3491100
3.44-3.5430.1332621.411100
3.54-3.6530.1272921.515199.7
3.65-3.7830.112831.8111100
3.78-3.9430.112752.1641100
3.94-4.112.90.0862811.908199.6
4.11-4.3330.0732851.599199.7
4.33-4.62.90.0632811.7141100
4.6-4.962.90.0552781.7321100
4.96-5.462.90.0452971.722199.7
5.46-6.242.80.0472801.832198.6
6.24-7.862.80.052851.764196.6
7.86-502.70.0533032.973196.8

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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 2HOJ

2hoj


Resolution: 2.9→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2573 549 9.7 %
Rwork0.1997 4709 -
obs-5258 92.5 %
Solvent computationBsol: 37.8982 Å2
Displacement parametersBiso max: 136.88 Å2 / Biso mean: 76.7559 Å2 / Biso min: 36.47 Å2
Baniso -1Baniso -2Baniso -3
1-4.636 Å20 Å20 Å2
2--4.636 Å20 Å2
3----9.271 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1665 20 8 1693
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_scbond_it1.6292
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scangle_it2.6152.5
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 DIFFRACTION5hypcns.par

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