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- PDB-4gxy: RNA structure -

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Basic information

Entry
Database: PDB / ID: 4gxy
TitleRNA structure
ComponentsAdenosylcobalamin riboswitch
KeywordsRNA / Riboswitch / adenosylcobalamin
Function / homologyAdenosylcobalamin / IRIDIUM HEXAMMINE ION / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.05 Å
AuthorsSerganov, A. / Peselis, A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structural insights into ligand binding and gene expression control by an adenosylcobalamin riboswitch.
Authors: Peselis, A. / Serganov, A.
History
DepositionSep 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Adenosylcobalamin riboswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,45812
Polymers56,1871
Non-polymers5,27111
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.633, 96.633, 132.684
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: RNA chain Adenosylcobalamin riboswitch


Mass: 56187.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: In vitro transcription
#2: Chemical ChemComp-B1Z / Adenosylcobalamin / Cobamamide


Mass: 1580.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C72H101CoN18O17P / Comment: medication*YM
#3: Chemical
ChemComp-IRI / IRIDIUM HEXAMMINE ION


Mass: 294.400 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: H18IrN6
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.18 Å3/Da / Density % sol: 61.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 240 mM sodium malonate, 22 % PEG3350 , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 1.1049 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 10, 2012
RadiationMonochromator: Single crystal bender / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1049 Å / Relative weight: 1
ReflectionResolution: 3.05→30 Å / Num. all: 14103 / Num. obs: 13827 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.20099 / Net I/σ(I): 26.6
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.6 / % possible all: 99.1

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Processing

Software
NameVersionClassification
MAR345data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.05→27.347 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 24.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2503 688 5 %Random
Rwork0.2081 ---
obs0.2102 13762 97.58 %-
all-14103 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.195 Å2 / ksol: 0.309 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.1826 Å20 Å20 Å2
2---8.1826 Å20 Å2
3---16.3652 Å2
Refinement stepCycle: LAST / Resolution: 3.05→27.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 3506 178 1 3685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064107
X-RAY DIFFRACTIONf_angle_d1.1896452
X-RAY DIFFRACTIONf_dihedral_angle_d18.1532011
X-RAY DIFFRACTIONf_chiral_restr0.063830
X-RAY DIFFRACTIONf_plane_restr0.008187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0503-3.28540.29761400.25582592X-RAY DIFFRACTION98
3.2854-3.61540.2631590.21222566X-RAY DIFFRACTION98
3.6154-4.1370.25331210.19912618X-RAY DIFFRACTION98
4.137-5.20630.24331260.19462633X-RAY DIFFRACTION98
5.2063-27.34770.23971420.20912665X-RAY DIFFRACTION95

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