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

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Basic information

Entry
Database: PDB / ID: 2hoo
TitleCrystal structure of an E. coli thi-box riboswitch bound to benfotiamine
Componentsthi-box riboswitch
KeywordsRNA / riboswitch / Benfotiamine
Function / homologyS-BENZOYLTHIAMINE O-MONOPHOSPHATE / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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.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.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_conn.ptnr2_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: thi-box riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5489
Polymers26,7991
Non-polymers7498
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.400, 61.400, 102.900
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: 26798.936 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-BFT / S-BENZOYLTHIAMINE O-MONOPHOSPHATE / BENFOTIAMINE


Mass: 468.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25N4O6PS / Comment: medication*YM
#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: 2.09 Å3/Da / Density % sol: 41.09 %
Crystal growTemperature: 295 K / pH: 6
Details: growth: 29% PEG 2000, 0.2 M NH4Cl, 8 mM CaCl2, 0.2 mM Na2WO4, 50 mM cacodylate pH 6.0; 0.25 mM BzTP, 0.25 mM spermine, 1.5 mM MgCl2, 50 mM KCl; cryo: above with 15% w/v sucrose; 600 x 70 x ...Details: growth: 29% PEG 2000, 0.2 M NH4Cl, 8 mM CaCl2, 0.2 mM Na2WO4, 50 mM cacodylate pH 6.0; 0.25 mM BzTP, 0.25 mM spermine, 1.5 mM MgCl2, 50 mM KCl; cryo: above with 15% w/v sucrose; 600 x 70 x 70 um xtal, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 6.00
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 200011
2CaCl211
3NH4Cl11
4MgCl211
5KCl11
6Na2WO411
7spermine11
8cacodylate11
9BzTP11
10PEG 200012
11CaCl212
12NH4Cl12
13MgCl212
14KCl12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.214698
DetectorDetector: CCD / Date: Feb 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.214698 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 4293 / % possible obs: 98.1 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 19.1
Reflection shellResolution: 3→3.1 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 2.5 / % possible all: 87.7

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.275 450 -RANDOM
Rwork0.212 ---
obs0.212 4293 92.9 %-
all-4622 --
Displacement parametersBiso mean: 80.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1695 38 3 1736
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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