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- PDB-3diz: Crystallization of the Thermotoga maritima lysine riboswitch boun... -

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Basic information

Entry
Database: PDB / ID: 3diz
TitleCrystallization of the Thermotoga maritima lysine riboswitch bound to lysine in the Absence of Mg2+
ComponentsRNA (174-MER)
KeywordsRNA / riboswitch / lysine
Function / homology: / LYSINE / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.85 Å
AuthorsSerganov, A.A.
CitationJournal: Nature / Year: 2008
Title: Structural insights into amino acid binding and gene control by a lysine riboswitch.
Authors: Serganov, A. / Huang, L. / Patel, D.J.
History
DepositionJun 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 / 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.pdbx_leaving_atom_flag / _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.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: RNA (174-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,09815
Polymers56,6361
Non-polymers46214
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.000, 78.803, 140.631
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain RNA (174-MER)


Mass: 56635.598 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: In vitro transcribed RNA from the Thermotoga maritima MSB8 asd gene
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 18% PEG 4000, 0.1M Sodium Citrate, 20% isopropanol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2Sodium Citrate11
3isopropanol11
4PEG 400012
5Sodium Citrate12
6isopropanol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.85→20 Å / Num. all: 15344 / Num. obs: 13349 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 15.7
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1489 / % possible all: 89.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 3DIL

3dil


Resolution: 2.85→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 34.921 / SU ML: 0.306 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: tls / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24388 639 5 %RANDOM
Rwork0.19278 ---
all0.19548 13826 --
obs0.19548 12048 87.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.32 Å2
Baniso -1Baniso -2Baniso -3
1--3.43 Å20 Å20 Å2
2---4.6 Å20 Å2
3---8.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.306 Å
Refinement stepCycle: LAST / Resolution: 2.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3752 23 10 3785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0214209
X-RAY DIFFRACTIONr_angle_refined_deg1.3282.9996569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.992154
X-RAY DIFFRACTIONr_chiral_restr0.0660.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021838
X-RAY DIFFRACTIONr_nbd_refined0.1720.21718
X-RAY DIFFRACTIONr_nbtor_refined0.270.22661
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2151
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.211
X-RAY DIFFRACTIONr_mcbond_it0.2071.55
X-RAY DIFFRACTIONr_mcangle_it0.40627
X-RAY DIFFRACTIONr_scbond_it0.55534444
X-RAY DIFFRACTIONr_scangle_it0.8694.56562
LS refinement shellResolution: 2.85→2.923 Å / Rfactor Rfree error: 0.415 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 50 -
Rwork0.37 886 -
obs-891 90.87 %
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)
10.97250.52970.41713.0015-0.27632.4230.18190.2583-0.1959-0.5553-0.0275-0.27050.5971-0.3099-0.15440.06060.0291-0.0085-0.07480.0311-0.122929.371-1.77918.673
21.2462-0.20380.60.56150.05491.4027-0.19640.05780.52360.0230.03720.0844-0.5479-0.3430.15930.10560.0687-0.0067-0.06620.0530.15767.08947.21320.96
32.8273-0.2260.98060.2112-0.07190.56870.05680.1332-0.273-0.0678-0.02540.3823-0.0903-0.0828-0.0314-0.03240.0277-0.0154-0.0343-0.0265-0.05578.60127.20611.009
44.317-1.7001-0.43250.91170.39230.26560.04540.32230.4559-0.137-0.1033-0.3614-0.11290.02640.0579-0.03090.019-0.0126-0.09390.0724-0.054229.6233.67414.981
56.43910.1979-2.15091.08980.33011.0362-0.4221-0.4757-0.89260.1185-0.0175-0.66810.38410.00550.4396-0.08050.05560.03840.00710.09350.312650.1488.69815.548
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 111 - 11
2X-RAY DIFFRACTION1AA163 - 174163 - 174
3X-RAY DIFFRACTION2AA12 - 7912 - 79
4X-RAY DIFFRACTION3AA80 - 11380 - 113
5X-RAY DIFFRACTION4AA114 - 140114 - 140
6X-RAY DIFFRACTION5AA141 - 162141 - 162

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