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- PDB-4lx5: X-ray crystal structure of the M6" riboswitch aptamer bound to py... -

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Basic information

Entry
Database: PDB / ID: 4lx5
TitleX-ray crystal structure of the M6" riboswitch aptamer bound to pyrimido[4,5-d]pyrimidine-2,4-diamine (PPDA)
ComponentsMutated adenine riboswitch aptamer
KeywordsRNA / Riboswitch / Gene expression platform
Function / homologypyrimido[4,5-d]pyrimidine-2,4-diamine / : / RNA / RNA (> 10)
Function and homology information
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 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 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 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.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.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

Downloads & links

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Assembly

Deposited unit
A: Mutated adenine riboswitch aptamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9456
Polymers22,6851
Non-polymers2595
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.050, 149.710, 24.400
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: 22685.416 Da / Num. of mol.: 1 / Mutation: U28G, G42C, U47C, U51C / Source method: obtained synthetically / Details: in vitro transcription / Source: (synth.) Vibrio vulnificus (bacteria) / References: GenBank: AE016796
#2: Chemical ChemComp-29G / pyrimido[4,5-d]pyrimidine-2,4-diamine


Mass: 162.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N6
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 17 / 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: 1.97 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 3M 1,6 hexanediol, 0.1M Tris (pH 9.0) , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / 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: 2.13→46.6 Å / Num. all: 10788 / Num. obs: 10766 / % possible obs: 99.8 % / Observed criterion σ(F): 2.13 / Observed criterion σ(I): 2.13 / Biso Wilson estimate: 59.89 Å2

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Processing

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

3la5


Resolution: 2.13→46.6 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.31 / σ(F): 1.34 / Phase error: 32.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2567 513 4.78 %
Rwork0.199 --
obs0.2017 10722 99.72 %
all-10788 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.9851 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.13→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1502 16 17 1535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051690
X-RAY DIFFRACTIONf_angle_d0.9862626
X-RAY DIFFRACTIONf_dihedral_angle_d14.301849
X-RAY DIFFRACTIONf_chiral_restr0.042355
X-RAY DIFFRACTIONf_plane_restr0.00672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.34440.40411290.30632487X-RAY DIFFRACTION100
2.3444-2.68360.38631280.29822501X-RAY DIFFRACTION100
2.6836-3.38090.29191290.22972529X-RAY DIFFRACTION100
3.3809-46.62310.2121270.16512692X-RAY DIFFRACTION99
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)
10.4992-1.01420.45512.1474-1.03490.43470.93230.3378-1.80820.2536-0.8803-1.3741-0.2482-0.3313-0.11850.22480.19090.00020.4613-0.10251.486610.59966.29964.2192
21.8647-1.43581.4035.2275-0.84671.59430.33370.2030.0509-0.4239-0.08790.5065-0.01130.0015-0.08330.36590.04260.00280.4249-0.0050.4539-10.143230.0316-4.9918
31.9677-0.40441.37322.43340.84551.5562-0.0558-0.38280.07321.61460.6221-1.79-0.44520.5864-0.65460.77390.0721-0.18780.7477-0.1510.632811.215721.42869.8235
42.9439-0.38181.45756.77220.29493.268-0.0580.52490.0241-0.65710.06191.7154-0.38750.1595-0.0810.52590.0056-0.17790.3766-0.07390.3999-9.345317.3554-6.8239
53.3889-1.4258-0.10981.6521.45582.080.33080.1962-1.2908-0.766-0.58382.965-0.2008-0.874-0.08870.40740.0709-0.28730.42030.04971.1362-20.449922.7089-3.6732
61.3208-1.17540.78317.45911.15383.4127-0.17130.1758-1.42730.1470.4641-1.01270.439-0.3498-0.19360.27050.01760.04380.5768-0.13140.931413.24796.10744.2547
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 46 )
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 51 )
4X-RAY DIFFRACTION4chain 'A' and (resid 52 through 61 )
5X-RAY DIFFRACTION5chain 'A' and (resid 62 through 72 )
6X-RAY DIFFRACTION6chain 'A' and (resid 73 through 83 )

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