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- PDB-3d2x: Structure of the thiamine pyrophosphate-specific riboswitch bound... -

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Basic information

Entry
Database: PDB / ID: 3d2x
TitleStructure of the thiamine pyrophosphate-specific riboswitch bound to oxythiamine pyrophosphate
ComponentsTPP-specific riboswitch
KeywordsRNA / riboswitch / thiamine pyrophosphate / oxythiamine pyrophosphate / antibiotic / drugs / complex
Function / homologyChem-D2X / RNA / RNA (> 10)
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsThore, S. / Frick, C. / Ban, N.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch
Authors: Thore, S. / Frick, C. / Ban, N.
History
DepositionMay 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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.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: TPP-specific riboswitch
B: TPP-specific riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,08617
Polymers49,9182
Non-polymers1,16915
Water2,270126
1
A: TPP-specific riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5559
Polymers24,9591
Non-polymers5968
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TPP-specific riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5318
Polymers24,9591
Non-polymers5727
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.497, 111.172, 55.375
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: RNA chain TPP-specific riboswitch


Mass: 24958.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid details: In vitro transcription / Production host: cell-free synthesis (others)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-D2X / 3-[(4-hydroxy-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium


Mass: 426.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18N3O8P2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 47.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 12-18% 1,6-hexanediol, 0.5mM spermine, 10mM magnesium sulfate, 40mM sodium cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
11,6-hexanediol11
21,6-hexanediol12
3spermine11
4magnesium sulfate11
5magnesium sulfate12
6sodium cacodylate11
7sodium cacodylate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 11, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. all: 16736 / Num. obs: 16268 / % possible obs: 97.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 42.3 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 14.6
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 2.85 / Num. unique all: 934 / % possible all: 97.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2cky

2cky


Resolution: 2.5→15 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 814 -RANDOM
Rwork0.233 ---
obs0.254 16268 97.8 %-
all-16634 --
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3312 65 126 3503

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