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- PDB-3q3z: Structure of a c-di-GMP-II riboswitch from C. acetobutylicum boun... -

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Basic information

Entry
Database: PDB / ID: 3q3z
TitleStructure of a c-di-GMP-II riboswitch from C. acetobutylicum bound to c-di-GMP
Componentsc-di-GMP-II riboswitch
KeywordsRNA / riboswitch / c-di-GMP
Function / homologyChem-C2E / RNA / RNA (> 10)
Function and homology information
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.51 Å
AuthorsSmith, K.D. / Shanahan, C.A. / Moore, E.L. / Simon, A.C. / Strobel, S.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural basis of differential ligand recognition by two classes of bis-(3'-5')-cyclic dimeric guanosine monophosphate-binding riboswitches.
Authors: Smith, K.D. / Shanahan, C.A. / Moore, E.L. / Simon, A.C. / Strobel, S.A.
History
DepositionDec 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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_conn.ptnr2_label_seq_id / _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
V: c-di-GMP-II riboswitch
A: c-di-GMP-II riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,76819
Polymers48,6912
Non-polymers3,07817
Water3,171176
1
V: c-di-GMP-II riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,89610
Polymers24,3451
Non-polymers1,5519
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: c-di-GMP-II riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8729
Polymers24,3451
Non-polymers1,5278
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.644, 70.285, 86.037
Angle α, β, γ (deg.)90.00, 98.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain c-di-GMP-II riboswitch / c-di-GMP-II aptamer


Mass: 24345.283 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: RNA WAS PREPARED BY IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE
Source: (synth.) Clostridium acetobutylicum (bacteria)
#2: Chemical
ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate


Mass: 690.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 13% PEG8000, 200 mM magnesium acetate, 100 mM sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 26, 2010
RadiationMonochromator: double crystal monochromator with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 15422 / Num. obs: 15422 / % possible obs: 98.1 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.4
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CBASSdata collection
SHELXSphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.51→38.07 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 1 / SU B: 19.593 / SU ML: 0.233 / σ(F): 0 / ESU R: 1.77 / ESU R Free: 0.299
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 791 5.1 %RANDOM
Rwork0.178 14629 --
obs0.1811 15420 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 141.31 Å2 / Biso mean: 66.9397 Å2 / Biso min: 35.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å20.27 Å2
2--4.18 Å2-0 Å2
3----4.2 Å2
Refinement stepCycle: LAST / Resolution: 2.51→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3224 197 176 3597
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0213861
X-RAY DIFFRACTIONr_bond_other_d0.0010.021343
X-RAY DIFFRACTIONr_angle_refined_deg1.172.9976032
X-RAY DIFFRACTIONr_angle_other_deg0.8233439
X-RAY DIFFRACTIONr_chiral_restr0.0450.2780
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021668
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02378
X-RAY DIFFRACTIONr_scbond_it3.393123861
X-RAY DIFFRACTIONr_scangle_it4.464166030
LS refinement shellResolution: 2.507→2.572 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 50 -
Rwork0.349 1082 -
all-1132 -
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)
13.47190.9964-0.31491.6359-0.07321.49740.1271-0.1627-0.0430.1204-0.0608-0.0110.11550.0799-0.06630.09540.0002-0.0295-0.0012-0.00260.0516-4.4099.843-23.8631
22.5392-0.7198-0.82751.91160.72381.73010.13180.3235-0.0079-0.141-0.1157-0.0076-0.0693-0.0986-0.01610.05730.0082-0.04150.03310.01490.0551-6.51737.226217.6804
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 75
2X-RAY DIFFRACTION2V7 - 75

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