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- PDB-4yaz: 3',3'-cGAMP riboswitch bound with 3',3'-cGAMP -

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Basic information

Entry
Database: PDB / ID: 4yaz
Title3',3'-cGAMP riboswitch bound with 3',3'-cGAMP
ComponentsRNA (84-MER)
KeywordsRNA / riboswitch / 3' / 3'-cGAMP / spinach / RNA structure / c-di-GMP
Function / homologyChem-4BW / : / RNA / RNA (> 10)
Function and homology information
Biological speciesGeobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRen, A.M. / Patel, D.J. / Rajashankar, R.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1 U19 CA179564 United States
CitationJournal: Cell Rep / Year: 2015
Title: Structural Basis for Molecular Discrimination by a 3',3'-cGAMP Sensing Riboswitch.
Authors: Ren, A. / Wang, X.C. / Kellenberger, C.A. / Rajashankar, K.R. / Jones, R.A. / Hammond, M.C. / Patel, D.J.
History
DepositionFeb 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Jul 22, 2015Group: Non-polymer description
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.conn_type_id / _struct_conn.id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
R: RNA (84-MER)
A: RNA (84-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,26612
Polymers54,6792
Non-polymers1,58810
Water3,225179
1
R: RNA (84-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1898
Polymers27,3391
Non-polymers8507
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: RNA (84-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0774
Polymers27,3391
Non-polymers7383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.623, 50.517, 78.657
Angle α, β, γ (deg.)90.00, 90.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: RNA chain RNA (84-MER)


Mass: 27339.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter (bacteria)
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-4BW / 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one / 3',3' cGAMP / c-GMP-AMP / c[G(3',5')pA(3',5')p]


Mass: 674.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O13P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M Na/K-phosphate, pH 6.2-6.6, 0.2 M NaCl and 40-45% PEG400.
PH range: 6.2-6.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→78.3 Å / Num. obs: 32313 / % possible obs: 98.3 % / Observed criterion σ(I): 1.6 / Redundancy: 3.3 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.16 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.6 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IRW

3irw


Resolution: 2→42.504 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2496 1484 5.09 %
Rwork0.2125 --
obs0.2144 29171 81.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→42.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3624 98 179 3901
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014176
X-RAY DIFFRACTIONf_angle_d1.2026480
X-RAY DIFFRACTIONf_dihedral_angle_d21.8872106
X-RAY DIFFRACTIONf_chiral_restr0.049838
X-RAY DIFFRACTIONf_plane_restr0.008172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.06420.3869750.31031400X-RAY DIFFRACTION24
2.0642-2.1380.40181000.29291642X-RAY DIFFRACTION28
2.138-2.22360.33581100.28331871X-RAY DIFFRACTION31
2.2236-2.32480.29711030.28732086X-RAY DIFFRACTION35
2.3248-2.44730.30821330.29642401X-RAY DIFFRACTION40
2.4473-2.60060.32741590.31532720X-RAY DIFFRACTION46
2.6006-2.80140.38571410.30283010X-RAY DIFFRACTION50
2.8014-3.08320.30991600.26153022X-RAY DIFFRACTION51
3.0832-3.52920.21351520.16793095X-RAY DIFFRACTION51
3.5292-4.44560.18211650.14463093X-RAY DIFFRACTION51
4.4456-42.51370.17041860.15613347X-RAY DIFFRACTION56
Refinement TLS params.Method: refined / Origin x: 81.0664 Å / Origin y: -3.4857 Å / Origin z: 99.0224 Å
111213212223313233
T0.1997 Å2-0.0639 Å20.0362 Å2-0.1556 Å2-0.0202 Å2--0.165 Å2
L0.9173 °20.1581 °20.2803 °2-0.403 °20.2405 °2--0.4908 °2
S-0.066 Å °0.1114 Å °-0.1387 Å °-0.082 Å °0.029 Å °0.0078 Å °-0.0646 Å °0.0665 Å °0.0275 Å °
Refinement TLS groupSelection details: all

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