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- PDB-3oxd: Crystal structure of glycine riboswitch with two mutations -

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Basic information

Entry
Database: PDB / ID: 3oxd
TitleCrystal structure of glycine riboswitch with two mutations
Components(domain II of glycine riboswitch) x 2
KeywordsRNA / Gene expression regulator / glycine riboswitch
Function / homology: / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.999 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_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)58,21736
Polymers57,3902
Non-polymers82634
Water1,26170
1
A: domain II of glycine riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,19720
Polymers28,7351
Non-polymers46219
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: domain II of glycine riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,02016
Polymers28,6551
Non-polymers36515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-262 kcal/mol
Surface area27060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.969, 83.969, 199.998
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#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
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE ORIGINAL MG CHAIN IDS HAVE BEEN CHANGED TO THE CLOSEST POLYMER CHAIN. 100 HAS BEEN ADDED TO THE ...THE ORIGINAL MG CHAIN IDS HAVE BEEN CHANGED TO THE CLOSEST POLYMER CHAIN. 100 HAS BEEN ADDED TO THE ORIGINAL MG RESIDUE 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: 3.55 Å3/Da / Density % sol: 65.32 %
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: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2009
RadiationMonochromator: SI mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.999→20 Å / Num. all: 16987 / Num. obs: 16953 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 41.5
Reflection shellResolution: 2.999→3.11 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 5.2 / % possible all: 99.9

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Processing

Software
NameClassification
CBASSdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementStarting model: PDB ENTRY 3OWI

3owi


Resolution: 2.999→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.938 / SU B: 29.308 / SU ML: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.661 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21404 857 5.1 %RANDOM
Rwork0.19558 ---
all0.1965 16102 --
obs0.1965 16063 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.102 Å2
Refinement stepCycle: LAST / Resolution: 2.999→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3785 34 70 3889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0214308
X-RAY DIFFRACTIONr_angle_refined_deg1.06436769
X-RAY DIFFRACTIONr_chiral_restr0.0470.2872
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021857
X-RAY DIFFRACTIONr_scbond_it0.56334308
X-RAY DIFFRACTIONr_scangle_it0.9774.56769
LS refinement shellResolution: 2.999→3.075 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 63 -
Rwork0.313 1107 -
obs--98.9 %
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)
13.17420.2102-0.72740.1209-0.13770.2471-0.11620.4993-0.593-0.04710.0211-0.02950.0722-0.11350.09510.1618-0.06070.02250.5445-0.16140.3507-5.109-46.31410.656
20.4753-0.1293-0.26280.1204-0.06090.44560.0417-0.00680.15480.0360.09830.0232-0.2601-0.1134-0.140.3367-0.01970.03430.39590.01960.2849-5.325-26.03222.76
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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