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- PDB-3skz: Crystal structure of the 2'- deoxyguanosine riboswitch bound to g... -

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Basic information

Entry
Database: PDB / ID: 3skz
TitleCrystal structure of the 2'- deoxyguanosine riboswitch bound to guanosine
ComponentsRNA (68-MER)
KeywordsRNA / three-way junction / riboswitch / 2'-deoxy guanosine
Function / homologyGUANOSINE / SUCCINIC ACID / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.605 Å
AuthorsPikovskaya, O. / Polonskaia, A. / Patel, D.J. / Serganov, A.
CitationJournal: Nat.Chem.Biol. / Year: 2011
Title: Structural principles of nucleoside selectivity in a 2'-deoxyguanosine riboswitch.
Authors: Pikovskaya, O. / Polonskaia, A. / Patel, D.J. / Serganov, A.
History
DepositionJun 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Feb 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
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (68-MER)
B: RNA (68-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,56416
Polymers44,0382
Non-polymers1,52614
Water1267
1
A: RNA (68-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9259
Polymers22,0191
Non-polymers9068
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RNA (68-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6397
Polymers22,0191
Non-polymers6206
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.806, 47.208, 227.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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RNA chain , 1 types, 2 molecules AB

#1: RNA chain RNA (68-MER)


Mass: 22018.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: in vitro transcribed RNA

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Non-polymers , 5 types, 21 molecules

#2: Chemical ChemComp-GMP / GUANOSINE


Mass: 283.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O5 / Details: in vitro transcribed RNA
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.05 M Na-succinate, ~3.0 M ammonium sulfate, 0.5 mM spermine and 20 mM magnesium chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 12208 / Num. obs: 11024 / % possible obs: 90.3 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 39
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 7.8 / Num. unique all: 1046 / % possible all: 87.2

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.605→20 Å / SU ML: 0.46 / σ(F): 1.89 / Phase error: 34.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2751 520 4.77 %
Rwork0.2194 --
obs0.2221 10910 89.51 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.61 Å2 / ksol: 0.337 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.7938 Å20 Å2-0 Å2
2--34.9925 Å2-0 Å2
3----26.1987 Å2
Refinement stepCycle: LAST / Resolution: 2.605→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2908 88 7 3003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063328
X-RAY DIFFRACTIONf_angle_d15175
X-RAY DIFFRACTIONf_dihedral_angle_d22.0251657
X-RAY DIFFRACTIONf_chiral_restr0.059684
X-RAY DIFFRACTIONf_plane_restr0.007141
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6047-2.86610.5271380.3962394X-RAY DIFFRACTION85
2.8661-3.27930.30541130.2592327X-RAY DIFFRACTION82
3.2793-4.12560.23711340.20132626X-RAY DIFFRACTION91
4.1256-20.03360.21331350.16993043X-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)
10.02410.0231-0.03190.1230.05230.09740.2219-0.1179-0.1122-0.05460.1691-0.216-0.09540.06550.23870.4770.07670.02440.80710.09080.34270.4428-1.391322.4553
20.3478-0.1187-0.43240.04230.14010.5510.05430.1165-0.0948-0.29750.199-0.0725-0.4050.01810.14280.47180.03450.07840.6741-0.03010.36271.4940.769126.6713
30.2746-0.19830.11140.89-0.29490.1165-0.069-0.3583-0.1310.31160.11440.0115-0.24570.05250.58350.2651-0.13030.03920.4763-0.09620.24569.12311.8765-3.9012
40.0025-0.0125-0.01010.22580.16810.12510.1434-0.0286-0.00180.3396-0.028-0.06670.151-0.23590.13160.3953-0.0581-0.00160.6876-0.06330.2334-4.6414-3.0737-3.3964
50.6503-0.41280.24672.07960.55980.37880.1336-0.02290.1209-0.25820.0597-0.335-0.11730.12720.21530.4789-0.06750.08720.48920.22380.45611.28150.523-68.6889
60.0179-0.1051-0.06510.64230.40650.25920.0939-0.09430.12070.18880.0154-0.25540.1711-0.01010.1950.2434-0.1007-0.0390.42310.18720.30132.35-0.8187-72.7823
70.23940.25630.16640.42230.10510.1571-0.096-0.03750.1692-0.22470.25610.2113-0.222-0.08040.2280.15170.0581-0.02140.1444-0.03070.18649.597-3.0693-41.9137
80.0559-0.0592-0.00080.11620.01860.059-0.0623-0.2075-0.00470.00080.1557-0.10410.0115-0.07460.14120.09210.1090.21130.8398-0.07420.0867-4.56341.211-42.1991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 22:30)
2X-RAY DIFFRACTION2(chain A and resid 81:89)
3X-RAY DIFFRACTION3(chain A and resid 31:47)
4X-RAY DIFFRACTION4(chain A and resid 61:80)
5X-RAY DIFFRACTION5(chain B and resid 22:30)
6X-RAY DIFFRACTION6(chain B and resid 81:89)
7X-RAY DIFFRACTION7(chain B and resid 31:47)
8X-RAY DIFFRACTION8(chain X and resid 61:80)

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