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- PDB-2hoj: Crystal structure of an E. coli thi-box riboswitch bound to thiam... -

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Basic information

Entry
Database: PDB / ID: 2hoj
TitleCrystal structure of an E. coli thi-box riboswitch bound to thiamine pyrophosphate, manganese ions
Componentsthi-box riboswitch
KeywordsRNA / riboswitch
Function / homology: / THIAMINE DIPHOSPHATE / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsEdwards, T.E. / Ferre-D'Amare, A.R.
CitationJournal: Structure / Year: 2006
Title: Crystal Structures of the Thi-Box Riboswitch Bound to Thiamine Pyrophosphate Analogs Reveal Adaptive RNA-Small Molecule Recognition
Authors: Edwards, T.E. / Ferre-D'Amare, A.R.
History
DepositionJul 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: thi-box riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,99416
Polymers26,8611
Non-polymers1,13315
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.700, 64.700, 101.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
DetailsThe biological assembly is a monomer

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Components

#1: RNA chain thi-box riboswitch


Mass: 26860.900 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: in vitro T7 RNA polymerase with 5'cis-hammerhead ribozyme and 5'-trans VS ribozyme
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: grown: 26% PEG 2000, 10 mM MnCl2, 0.2 M NH4Cl, 50 mM cacodylate pH 6.0; 1.5 mM MgCl2, 0.5 mM TPP, 50 mM KCl, 0.25 mM spermine; cryo: above plus 15% Ficoll 400, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 200011
2MnCl211
3NH4Cl11
4MgCl211
5KCl11
6spermine11
7cacodylate11
8TPP11
9PEG 200012
10MnCl212
11NH4Cl12
12MgCl212
13KCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorDetector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 8298 / Num. obs: 8398 / % possible obs: 100 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.062
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.548 / Num. unique all: 758 / % possible all: 99.8

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 2.8 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.257 878 random
Rwork0.229 --
all-8656 -
obs-8398 -
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.74 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1661 40 22 1723
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.37

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