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

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Basic information

Entry
Database: PDB / ID: 3dir
TitleCrystallization of the Thermotoga maritima lysine riboswitch bound to N6-1-iminoethyl-L-Lysine
ComponentsRNA (174-MER)
KeywordsRNA / riboswitch / Lysine
Function / homologyN~6~-[(1Z)-ethanimidoyl]-L-lysine / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 20, 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 1.2Oct 21, 2020Group: Data collection / Derived calculations / Category: reflns_shell / struct_conn / struct_site
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_obs ..._reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_obs / _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
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)57,27514
Polymers56,7961
Non-polymers47913
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.805, 78.839, 143.318
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: 56795.555 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.: 11 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-IEL / N~6~-[(1Z)-ethanimidoyl]-L-lysine


Type: L-peptide linking / Mass: 187.239 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17N3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.73 Å3/Da / Density % sol: 54.87 %
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: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 13631 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 44.5
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 44.5 / Num. unique all: 1405 / Num. unique obs: 1159 / % possible all: 82.5

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Processing

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

3dil


Resolution: 2.9→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU ML: 0.264 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: tls / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21132 688 5.1 %RANDOM
Rwork0.17797 ---
all0.17966 13578 --
obs0.17966 12823 94.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Refine analyzeLuzzati coordinate error obs: 0.264 Å
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3760 25 11 3796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0214220
X-RAY DIFFRACTIONr_angle_refined_deg1.34536583
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021843
X-RAY DIFFRACTIONr_nbd_refined0.1580.21481
X-RAY DIFFRACTIONr_nbtor_refined0.2690.22571
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2131
X-RAY DIFFRACTIONr_metal_ion_refined0.1520.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.28
LS refinement shellResolution: 2.9→2.974 Å / Rfactor Rfree error: 0.346 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 36 -
Rwork0.37 793 -
obs-1009 82.16 %
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)
14.02282.61660.35867.4858-0.29213.93670.18090.3891-0.0901-0.67880.1452-0.00170.6675-0.1759-0.3261-0.09850.063-0.0852-0.11110.0569-0.163529.971-1.9419.092
21.5086-0.03980.66170.66860.51061.5506-0.20080.22120.7337-0.1866-0.0914-0.0394-0.6041-0.41390.29220.05330.1751-0.04240.08520.11760.24087.46747.20721.381
34.4128-1.11841.98010.472-1.07032.60180.06730.436-0.0513-0.0836-0.1890.3312-0.3501-0.0670.1217-0.01970.181-0.1764-0.0499-0.01080.09769.07127.15111.339
46.952-5.130.71345.5347-0.05611.05810.39260.39980.8504-0.5336-0.2969-0.6082-0.49670.0328-0.0958-0.0230.0757-0.0563-0.05140.09420.050830.20433.64415.519
512.30023.1476-2.27392.44380.63581.3254-0.264-0.3562-0.86730.3639-0.0779-0.5720.4520.21650.3419-0.07090.1724-0.08280.03620.07180.183451.0788.5516.052
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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