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- PDB-4lx6: X-ray crystal structure of the M6C" riboswitch aptamer bound to 2... -

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Basic information

Entry
Database: PDB / ID: 4lx6
TitleX-ray crystal structure of the M6C" riboswitch aptamer bound to 2-aminopyrimido[4,5-d]pyrimidin-4(3H)-one (PPAO)
ComponentsMutated adenine riboswitch aptamer
KeywordsRNA / Riboswitch Gene expression platform
Function / homology2-aminopyrimido[4,5-d]pyrimidin-4(3H)-one / : / RNA / RNA (> 10)
Function and homology information
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsDunstan, M.S. / Leys, D.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Modular riboswitch toolsets for synthetic genetic control in diverse bacterial species.
Authors: Robinson, C.J. / Vincent, H.A. / Wu, M.C. / Lowe, P.T. / Dunstan, M.S. / Leys, D. / Micklefield, J.
History
DepositionJul 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Sep 20, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

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Assembly

Deposited unit
A: Mutated adenine riboswitch aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9697
Polymers22,6841
Non-polymers2856
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.100, 151.690, 24.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: RNA chain Mutated adenine riboswitch aptamer


Mass: 22684.432 Da / Num. of mol.: 1 / Mutation: U28G, G42C, U47C, U51C, U74C / Source method: obtained synthetically / Details: in vitro transcription / Source: (synth.) Vibrio vulnificus (bacteria) / References: GenBank: AE016796
#2: Chemical ChemComp-29H / 2-aminopyrimido[4,5-d]pyrimidin-4(3H)-one


Mass: 163.137 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5N5O
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSynthetic construct from in vitro transcription

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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: 2.07 Å3/Da / Density % sol: 40.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 3M 1,6-hexanediol, 0.1 M tris ph9.0, 0.2 M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→47.5 Å / Num. all: 10992 / Num. obs: 10915 / % possible obs: 99.3 % / Observed criterion σ(F): 2.15 / Observed criterion σ(I): 2.15

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LA5

3la5


Resolution: 2.15→47.5 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / σ(F): 1.34 / Phase error: 35.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2548 523 4.8 %
Rwork0.2038 --
obs0.2064 10894 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.4802 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.15→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1502 17 22 1541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051690
X-RAY DIFFRACTIONf_angle_d0.912626
X-RAY DIFFRACTIONf_dihedral_angle_d12.416849
X-RAY DIFFRACTIONf_chiral_restr0.038355
X-RAY DIFFRACTIONf_plane_restr0.00772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.36640.38531130.28452525X-RAY DIFFRACTION100
2.3664-2.70880.36981440.29432569X-RAY DIFFRACTION100
2.7088-3.41260.24951130.22552577X-RAY DIFFRACTION99
3.4126-47.58410.22941530.17122700X-RAY DIFFRACTION98
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)
15.3765.0681-0.68384.785-0.64541.58921.54810.9021-0.0242-0.3869-0.75710.0073-0.0979-0.0727-0.89130.67120.0598-0.14110.65940.0192.056840.98682.293610.9049
21.66431.19420.07831.09790.94593.18830.6525-2.4014-2.81530.7216-0.1337-0.65860.5467-0.2246-0.44570.4328-0.1065-0.11750.76030.31050.881128.420213.699321.4627
31.4555-1.30070.19293.3839-1.39241.48510.21770.3997-0.1498-0.3348-0.01090.7568-0.10030.137-0.1830.29970.0179-0.05080.3316-0.07790.414814.138931.20927.1471
46.62370.41571.87664.72951.16313.10.09570.2678-0.8787-0.30780.15510.39650.15850.303-0.28970.3239-0.0236-0.01280.28780.01740.329322.272819.306710.5227
52.29030.9840.25020.66430.8582.05280.3342-0.3762-1.3576-0.2421-0.14112.1342-0.134-0.537-0.21980.38170.0642-0.14010.44330.08531.08934.204222.90598.6218
60.5077-1.8255-0.3756.73370.81232.00670.2365-0.2628-2.31460.30850.0031-0.82830.2693-0.3174-0.22330.3598-0.0375-0.12970.58940.01971.314438.17336.627416.1388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 24 )
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 46 )
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 61 )
5X-RAY DIFFRACTION5chain 'A' and (resid 62 through 72 )
6X-RAY DIFFRACTION6chain 'A' and (resid 73 through 83 )

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