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- PDB-2cky: Structure of the Arabidopsis thaliana thiamine pyrophosphate ribo... -

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Basic information

Entry
Database: PDB / ID: 2cky
TitleStructure of the Arabidopsis thaliana thiamine pyrophosphate riboswitch with its regulatory ligand
ComponentsNUCLEIC ACID
KeywordsNUCLEIC ACID
Function / homologyOSMIUM ION / THIAMINE DIPHOSPHATE / RNA / RNA (> 10)
Function and homology information
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsThore, S. / Leibundgut, M. / Ban, N.
CitationJournal: Science / Year: 2006
Title: Structure of the Eukaryotic Thiamine Pyrophosphate Riboswitch with its Regulatory Ligand.
Authors: Thore, S. / Leibundgut, M. / Ban, N.
History
DepositionApr 24, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUCLEIC ACID
B: NUCLEIC ACID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,29426
Polymers49,9182
Non-polymers3,37624
Water00
1
A: NUCLEIC ACID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,45712
Polymers24,9591
Non-polymers1,49811
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: NUCLEIC ACID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,83714
Polymers24,9591
Non-polymers1,87813
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.850, 98.670, 54.550
Angle α, β, γ (deg.)90.00, 104.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain NUCLEIC ACID


Mass: 24958.838 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ARABIDOPSIS THALIANA (thale cress)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-OS / OSMIUM ION


Mass: 190.230 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Os
#4: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S

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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: 2.57 Å3/Da / Density % sol: 51.8 %
Crystal growDetails: 10% 1,6-HEXANEDIOL 50MM SODIUM CACODYLATE PH7.0 10MM MGSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.1397
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1397 Å / Relative weight: 1
ReflectionResolution: 2.9→15 Å / Num. obs: 8918 / % possible obs: 96 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.235 / Rsym value: 0.175 / Net I/σ(I): 7.6
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.72 / % possible all: 74

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
SHELXphasing
SHARPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MAD / Resolution: 2.9→15 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.887 / SU B: 37.628 / SU ML: 0.345 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.474 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AN ALTERNATIVE CONFORMATION OF THE PYROPHOSPHATE THAT INCLUDES AN ADDITIONAL MG ION WOULD ALSO EXPLAIN THE ELECTRON DENSITY BUT DID NOT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AN ALTERNATIVE CONFORMATION OF THE PYROPHOSPHATE THAT INCLUDES AN ADDITIONAL MG ION WOULD ALSO EXPLAIN THE ELECTRON DENSITY BUT DID NOT REFINE STABLY AT CURRENT RESOLUTION. ATOM 3333 O22 TDP Z 1 -6.837 9.528 -43.442 1.00 57.26 ATOM 3334 P2 TDP Z 1 -5.700 8.586 -42.801 1.00 58.90 ATOM 3335 O23 TDP Z 1 -5.792 8.782 -41.205 1.00 56.67 ATOM 3336 O21 TDP Z 1 -5.840 7.175 -43.223 1.00 59.87 ATOM 3337 O11 TDP Z 1 -4.282 9.217 -43.230 1.00 58.47 ATOM 3338 P1 TDP Z 1 -3.766 10.572 -42.527 1.00 57.46 ATOM 3339 O13 TDP Z 1 -3.929 10.438 -40.935 1.00 57.28 ATOM 3340 O12 TDP Z 1 -4.348 11.782 -43.152 1.00 57.28 ATOM 3341 O5G TDP Z 1 -2.168 10.573 -42.729 1.00 56.65 ATOM 3342 C5B TDP Z 1 -1.596 9.973 -43.895 1.00 58.30 ATOM 3343 C5A TDP Z 1 -0.879 11.035 -44.733 1.00 58.55 ATOM 3344 C5 TDP Z 1 0.286 11.649 -43.960 1.00 57.40 ATOM 3345 C4 TDP Z 1 1.590 11.195 -43.763 1.00 56.88 ATOM 3346 C4A TDP Z 1 2.111 9.923 -44.433 1.00 58.41 ATOM 3347 S1 TDP Z 1 0.170 13.155 -43.100 1.00 63.43 ATOM 3348 C2 TDP Z 1 1.791 13.043 -42.459 1.00 58.90 ATOM 3349 N3 TDP Z 1 2.352 11.945 - 42.971 1.00 58.30 ATOM 3350 C35 TDP Z 1 3.742 11.569 -42.664 1.00 51.33 ATOM 3351 C5* TDP Z 1 4.667 12.074 -43.771 1.00 48.26 ATOM 3352 C6* TDP Z 1 4.096 12.728 -44.858 1.00 46.89 ATOM 3353 N1* TDP Z 1 4.858 13.191 -45.830 1.00 46.75 ATOM 3354 C2* TDP Z 1 6.191 13.046 -45.794 1.00 48.28 ATOM 3355 C2A TDP Z 1 7.051 13.632 -46.917 1.00 46.88 ATOM 3356 N3* TDP Z 1 6.783 12.419 -44.770 1.00 48.53 ATOM 3357 C4* TDP Z 1 6.048 11.929 -43.760 1.00 48.94 ATOM 3358 N4* TDP Z 1 6.649 11.292 - 42.759 1.00 48.13 ATOM 3359 MG MG M 1 -4.149 8.720 -39.392 1.00 48.53 ATOM 3360 MG MG M 2 -7.655 11.172 -43.838 1.00 68.69 ATOM 3361 O22 TDP Z 2 -1.323 -14.809-100.997 1.00 75.50 ATOM 3362 P2 TDP Z 2 -0.700 -13.758 -99.945 1.00 73.87 ATOM 3363 O23 TDP Z 2 0.797 -13.435-100.442 1.00 71.46 ATOM 3364 O21 TDP Z 2 -1.543 -12.551 -99.810 1.00 73.60 ATOM 3365 O11 TDP Z 2 -0.542 -14.553 -98.557 1.00 72.09 ATOM 3366 P1 TDP Z 2 0.607 -15.670 -98.393 1.00 71.83 ATOM 3367 O13 TDP Z 2 1.995 - 15.124 -98.985 1.00 71.01 ATOM 3368 O12 TDP Z 2 0.178 -17.018 -98.830 1.00 73.08 ATOM 3369 O5G TDP Z 2 0.854 -15.664 -96.804 1.00 69.28 ATOM 3370 C5B TDP Z 2 -0.265 -15.547 -95.922 1.00 69.80 ATOM 3371 C5A TDP Z 2 -0.542 -16.897 -95.257 1.00 71.58 ATOM 3372 C5 TDP Z 2 0.625 -17.307 -94.362 1.00 71.11 ATOM 3373 C4 TDP Z 2 1.021 -16.795 -93.126 1.00 70.49 ATOM 3374 C4A TDP Z 2 0.188 -15.742 -92.391 1.00 68.84 ATOM 3375 S1 TDP Z 2 1.775 -18.550 -94.770 1.00 74.34 ATOM 3376 C2 TDP Z 2 2.765 - 18.232 -93.367 1.00 72.30 ATOM 3377 N3 TDP Z 2 2.151 -17.298 - 92.637 1.00 70.45 ATOM 3378 C35 TDP Z 2 2.715 -16.846 -91.353 1.00 72.30 ATOM 3379 C5* TDP Z 2 2.073 -17.621 -90.204 1.00 62.80 ATOM 3380 C6* TDP Z 2 0.999 -18.455 -90.495 1.00 62.47 ATOM 3381 N1* TDP Z 2 0.373 -19.098 -89.528 1.00 61.62 ATOM 3382 C2* TDP Z 2 0.754 -18.967 -88.251 1.00 60.60 ATOM 3383 C2A TDP Z 2 0.029 -19.754 -87.159 1.00 60.95 ATOM 3384 N3* TDP Z 2 1.783 -18.172 -87.923 1.00 60.57 ATOM 3385 C4* TDP Z 2 2.451 -17.504 -88.871 1.00 62.25 ATOM 3386 N4* TDP Z 2 3.505 - 16.764 -88.539 1.00 61.96 ATOM 3387 MG MG M 3 3.095 -13.594 - 99.566 1.00 49.90 ATOM 3388 MG MG M 4 -1.296 -16.602-102.200 1.00 68.69
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1270 12.5 %RANDOM
Rwork0.183 ---
obs0.191 8918 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20 Å20.88 Å2
2---0.12 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3310 74 0 3384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213758
X-RAY DIFFRACTIONr_bond_other_d0.0030.021292
X-RAY DIFFRACTIONr_angle_refined_deg2.21835856
X-RAY DIFFRACTIONr_angle_other_deg1.42633360
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_restr0.0820.2770
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021654
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1780.2885
X-RAY DIFFRACTIONr_nbd_other0.2470.21728
X-RAY DIFFRACTIONr_nbtor_refined0.2520.21414
X-RAY DIFFRACTIONr_nbtor_other0.0950.2874
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2112
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3920.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.19535429
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0174.55856
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.97 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.439 73
Rwork0.355 469
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)
11.01410.98140.27422.76820.15542.1085-0.0123-0.0642-0.1056-0.4060.1671-0.0458-0.03490.1515-0.15480.21820.0301-0.09880.0666-0.03890.10215.2412.466-46.358
23.28590.0667-0.51353.34471.75885.06860.09470.1432-0.1806-0.7329-0.23080.164-0.3047-0.27290.13610.3374-0.0355-0.19730.04080.0890.1974-5.4474.163-51.447
30.6031-0.46280.26053.6733-0.81791.1279-0.1373-0.1238-0.07690.09720.04090.45750.0835-0.10090.09640.1859-0.0186-0.06670.1406-0.02090.1514-0.227-18.266-88.755
44.4041-1.0656-2.53253.77950.4984.9602-0.18030.5835-0.2484-0.3599-0.22591.0863-0.057-0.86110.40620.2822-0.0884-0.21890.1263-0.01570.3754-8.463-9.543-96.711
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 59
2X-RAY DIFFRACTION2A60 - 77
3X-RAY DIFFRACTION3B1 - 59
4X-RAY DIFFRACTION4B60 - 77

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