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- PDB-3oxm: crystal structure of glycine riboswitch, Tl-Acetate soaked -

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Basic information

Entry
Database: PDB / ID: 3oxm
Titlecrystal structure of glycine riboswitch, Tl-Acetate soaked
Components(domain II of glycine ...) x 2
KeywordsRNA / Gene expression regulator / glycine riboswitch
Function / homologyGLYCINE / THALLIUM (I) ION / : / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsHuang, L. / Serganov, A. / Patel, D.J.
CitationJournal: Mol.Cell / Year: 2010
Title: Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch.
Authors: Huang, L. / Serganov, A. / Patel, D.J.
History
DepositionSep 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_ref_seq_dif / 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.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_ref_seq_dif.details / _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: domain II of glycine riboswitch
B: domain II of glycine riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,24041
Polymers57,3902
Non-polymers2,85039
Water64936
1
A: domain II of glycine riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,22123
Polymers28,7351
Non-polymers1,48622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: domain II of glycine riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,01918
Polymers28,6551
Non-polymers1,36417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-285 kcal/mol
Surface area26790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.783, 83.783, 200.066
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Domain II of glycine ... , 2 types, 2 molecules AB

#1: RNA chain domain II of glycine riboswitch


Mass: 28735.090 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcription / References: GenBank: CP001485.1
#2: RNA chain domain II of glycine riboswitch


Mass: 28655.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: in vitro transcription / References: GenBank: CP001485.1

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Non-polymers , 4 types, 75 molecules

#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical
ChemComp-TL / THALLIUM (I) ION


Mass: 204.383 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Tl
#5: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE ORIGINAL MG AND TL CHAIN IDS HAVE BEEN CHANGED TO THE CLOSEST POLYMER CHAIN. 100 HAS BEEN ADDED ...THE ORIGINAL MG AND TL CHAIN IDS HAVE BEEN CHANGED TO THE CLOSEST POLYMER CHAIN. 100 HAS BEEN ADDED TO THE ORIGINAL MG and 200 HAS BEEN ADDED TO THE ORIGINAL TL RESIDUE NUMBERS.

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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: 3.53 Å3/Da / Density % sol: 65.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 0.05 M Na-cacodylate, pH 5.1, 0.2 M KCl, 8 % (w/v) PEG8000 and 80 mM magnesium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2009
RadiationMonochromator: SI mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.95→20 Å / Num. all: 17793 / Num. obs: 17793 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 47.7
Reflection shellResolution: 2.95→3 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.51 / Num. unique all: 881 / % possible all: 100

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Processing

Software
NameClassification
CBASSdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OWI

3owi


Resolution: 2.95→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.937 / SU B: 28.527 / SU ML: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22544 904 5.1 %RANDOM
Rwork0.19985 ---
all0.20111 16907 --
obs0.20111 16839 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.13 Å2
Refinement stepCycle: LAST / Resolution: 2.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3807 47 36 3890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0214308
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.02136732
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_restr0.0470.2877
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021876
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0941.58
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.16228
X-RAY DIFFRACTIONr_scbond_it0.57234300
X-RAY DIFFRACTIONr_scangle_it0.9954.56724
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 67 -
Rwork0.308 1198 -
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)
13.11830.1238-1.03110.0598-0.02570.4039-0.15530.5211-0.4767-0.0410.0529-0.0479-0.0139-0.10960.10240.0925-0.04640.00190.5929-0.13110.3771-5.109-46.31410.656
20.65250.0089-0.42240.0455-0.07430.4750.06440.04550.13230.03030.06450.0675-0.2593-0.1339-0.12890.35560.01360.01570.40450.04010.2949-5.325-26.03222.76
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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