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- PDB-2gdi: Crystal structure of thiamine pyrophosphate-specific riboswitch i... -

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Basic information

Entry
Database: PDB / ID: 2gdi
TitleCrystal structure of thiamine pyrophosphate-specific riboswitch in complex with thiamine pyrophosphate
ComponentsTPP riboswitch
KeywordsRNA / riboswitch / thiamine pyrophosphate
Function / homology: / THIAMINE DIPHOSPHATE / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsSerganov, A.
CitationJournal: Nature / Year: 2006
Title: Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch.
Authors: Serganov, A. / Polonskaia, A. / Phan, A.T. / Breaker, R.R. / Patel, D.J.
History
DepositionMar 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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_conn_type / 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_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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
X: TPP riboswitch
Y: TPP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,24415
Polymers52,0842
Non-polymers1,16013
Water5,621312
1
X: TPP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,70410
Polymers26,0421
Non-polymers6629
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Y: TPP riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5405
Polymers26,0421
Non-polymers4984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.819, 29.558, 95.170
Angle α, β, γ (deg.)90.00, 94.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

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RNA chain , 1 types, 2 molecules XY

#1: RNA chain TPP riboswitch


Mass: 26042.248 Da / Num. of mol.: 2 / Fragment: sensing domain / Source method: obtained synthetically / Details: RNA was prepared by in vitro transcription

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Non-polymers , 5 types, 325 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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 Å3/Da / Density % sol: 38.59 %
Crystal growTemperature: 293 K / pH: 6.9
Details: 28 % PEG4000, 100 mM Na-acetate, pH 4.8, and 200 mM NH4-acetate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.90

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONNSLS X2511.1
SYNCHROTRONNSLS X2521.1407, 1.1411, 1.1201
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 7, 2005
ADSC QUANTUM 3152CCDNov 7, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI 111 CHANNELSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.14071
31.14111
41.12011
ReflectionResolution: 2.05→20 Å / Num. obs: 27007 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.062
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.89 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CAD4data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.414 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1337 5 %RANDOM
Rwork0.208 ---
obs0.21 25258 99.8 %-
all-25309 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å20 Å2-2.37 Å2
2--1.81 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3442 63 312 3817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0213946
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.04336115
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1290.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021696
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1640.31548
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2840.52406
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.5449
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1410.57
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.351
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.517
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1991.52
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.43526
X-RAY DIFFRACTIONr_scbond_it0.8534151
X-RAY DIFFRACTIONr_scangle_it1.1964.56109
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 98 -
Rwork0.285 1850 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.5548-8.34243.123913.8257-0.12753.68370.44210.2056-0.0882-0.1476-0.5312-0.37180.4062-0.08910.08910.0322-0.02230.0404-0.07520.13770.0391-22.4481.057-25.338
26.81861.71471.06397.5176-1.96916.658-0.0598-0.02830.3076-0.2099-0.20760.1167-0.1825-0.22780.2674-0.02220.10080.0664-0.1142-0.0002-0.019340.036-0.18464.692
36.2186-0.81922.8263.5808-1.60463.3589-0.32490.58390.5866-0.3533-0.1552-0.3612-0.52170.42630.4801-0.1152-0.01540.0802-0.1640.0446-0.0329-15.897-1.114-7.928
45.0196-2.04822.32714.6454-0.85954.97860.29440.8711-0.6504-0.14260.143-0.08110.48150.7966-0.4373-0.07870.02930.03610.0993-0.12880.03824.8442.17255.213
50.98160.48670.24682.0990.18561.2610.1009-0.2134-0.09520.2772-0.0791-0.1273-0.18130.2004-0.0217-0.1446-0.02260.0807-0.12260.0177-0.0758-4.275-9.67211.187
63.11550.84794.3321.8549-0.1437.0998-0.05640.233-0.4193-0.36950.4038-0.15890.23290.2628-0.34740.0292-0.06560.04980.0736-0.10080.004111.01910.60738.865
72.84510.28330.18432.7122-0.48231.03770.0861-0.0418-0.1683-0.022-0.04830.08490.0096-0.0292-0.0378-0.19820.00590.0941-0.20370.0076-0.0451-25.223-15.6611.76
82.5407-0.82840.40151.6758-0.12642.7663-0.1894-0.0125-0.18060.18650.08060.0444-0.3455-0.07020.10880.02810.08440.05480.0856-0.0472-0.00610.96814.18162.492
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1XA10 - 141 - 5
2X-RAY DIFFRACTION1XA85 - 8976 - 80
3X-RAY DIFFRACTION2YB10 - 141 - 5
4X-RAY DIFFRACTION2YB85 - 8976 - 80
5X-RAY DIFFRACTION3XA15 - 206 - 11
6X-RAY DIFFRACTION3XA45 - 5136 - 42
7X-RAY DIFFRACTION4YB15 - 206 - 11
8X-RAY DIFFRACTION4YB45 - 5136 - 42
9X-RAY DIFFRACTION5XA21 - 4412 - 35
10X-RAY DIFFRACTION5XJ1031
11X-RAY DIFFRACTION6YB21 - 4412 - 35
12X-RAY DIFFRACTION6YM1131
13X-RAY DIFFRACTION7XA52 - 8443 - 75
14X-RAY DIFFRACTION7XH - I101 - 1021
15X-RAY DIFFRACTION7XC - G121 - 1251
16X-RAY DIFFRACTION7XN1001
17X-RAY DIFFRACTION8YB52 - 8443 - 75
18X-RAY DIFFRACTION8YK - L111 - 1121
19X-RAY DIFFRACTION8YO1001

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