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- PDB-3owz: Crystal structure of glycine riboswitch, soaked in Iridium -

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Basic information

Entry
Database: PDB / ID: 3owz
TitleCrystal structure of glycine riboswitch, soaked in Iridium
Components(Domain II of glycine ...) x 2
KeywordsRNA / gene expression / glycine riboswitch
Function / homologyGLYCINE / IRIDIUM HEXAMMINE ION / : / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.949 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 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 8, 2014Group: Structure summary
Revision 1.3Feb 21, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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)64,70043
Polymers57,3902
Non-polymers7,31041
Water1,27971
1
A: Domain II of glycine riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,53722
Polymers28,7351
Non-polymers3,80221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Domain II of glycine riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,16321
Polymers28,6551
Non-polymers3,50820
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12150 Å2
ΔGint-199 kcal/mol
Surface area25440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.610, 82.610, 149.550
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, 112 molecules

#3: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#5: Chemical...
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: H18IrN6
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

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Details

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

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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: 52.08 %
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: 1.1053,1.1056,1.1256,1.10859
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 10, 2009
RadiationMonochromator: SI mirror / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.10531
21.10561
31.12561
41.108591
ReflectionResolution: 2.949→20 Å / Num. all: 12933 / Num. obs: 12921 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 38
Reflection shellResolution: 2.949→3 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.385 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHARPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.949→20 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.906 / SU B: 14.223 / SU ML: 0.272 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23421 1280 9.9 %RANDOM
Rwork0.20966 ---
all0.21207 11703 --
obs0.21207 11610 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 2.949→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3703 181 71 3955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0214358
X-RAY DIFFRACTIONr_angle_refined_deg0.97636947
X-RAY DIFFRACTIONr_chiral_restr0.0420.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021827
X-RAY DIFFRACTIONr_mcbond_it0.0291.58
X-RAY DIFFRACTIONr_mcangle_it0.03928
X-RAY DIFFRACTIONr_scbond_it0.6934350
X-RAY DIFFRACTIONr_scangle_it1.1824.56939
LS refinement shellResolution: 2.949→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 80 -
Rwork0.28 826 -
obs--99.23 %

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