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

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Basic information

Entry
Database: PDB / ID: 2hop
TitleCrystal structure of an E. coli thi-box riboswitch bound to pyrithiamine
Componentsthi-box riboswitch
KeywordsRNA / riboswitch
Function / homologyChem-218 / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: thi-box riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1716
Polymers26,7991
Non-polymers3725
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.300, 61.300, 103.600
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-218 / 1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-(2-HYDROXYETHYL)-2-METHYLPYRIDINIUM


Mass: 259.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19N4O

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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: 2.1 Å3/Da / Density % sol: 41.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: grown: 30% PEG 2000, 0.2 M NH4Cl, 50 mM Bis-Tris pH 6.5, 15 mM CaCl2; 0.5 mM PT, 0.5 mM spermine, 100 mM KCl, 3 mM MgCl2; cryo: above with 20% sucrose; 680 x 80 x 80 um xtal., VAPOR ...Details: grown: 30% PEG 2000, 0.2 M NH4Cl, 50 mM Bis-Tris pH 6.5, 15 mM CaCl2; 0.5 mM PT, 0.5 mM spermine, 100 mM KCl, 3 mM MgCl2; cryo: above with 20% sucrose; 680 x 80 x 80 um xtal., VAPOR DIFFUSION, HANGING DROP, temperature 295K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 200011
2CaCl211
3NH4Cl11
4MgCl211
5KCl11
6Bis-Tris11
7spermine11
8PT11
9TPP11
10PEG 200012
11CaCl212
12NH4Cl12
13MgCl212
14KCl12
15Bis-Tris12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 25, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→15 Å / Num. all: 3231 / Num. obs: 2978 / % possible obs: 91.5 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 10.5
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 3.3 / Num. unique all: 303 / % possible all: 92.9

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.331 187 -random
Rwork0.251 ---
all-3455 --
obs-2934 84.9 %-
Displacement parametersBiso mean: 52.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.63 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a1.66 Å0.82 Å
Refinement stepCycle: LAST / Resolution: 3.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1561 23 0 1584
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.23

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