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- PDB-3ds7: Structure of an RNA-2'-deoxyguanosine complex -

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Basic information

Entry
Database: PDB / ID: 3ds7
TitleStructure of an RNA-2'-deoxyguanosine complex
Components67-MER
KeywordsRNA / RNA-ligand complex / riboswitch
Function / homologyACETATE ION / 2'-DEOXY-GUANOSINE / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsEdwards, A.L. / Batey, R.T.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: A structural basis for the recognition of 2'-deoxyguanosine by the purine riboswitch.
Authors: Edwards, A.L. / Batey, R.T.
History
DepositionJul 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 67-MER
B: 67-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,51117
Polymers43,0862
Non-polymers2,42515
Water11,205622
1
A: 67-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6758
Polymers21,5431
Non-polymers1,1327
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 67-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8369
Polymers21,5431
Non-polymers1,2938
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.139, 41.830, 64.810
Angle α, β, γ (deg.)86.55, 81.16, 89.64
Int Tables number1
Space group name H-MP1

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Components

#1: RNA chain 67-MER


Mass: 21542.873 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence is synthetic derived from a mutagenesis study
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CoH18N6
#4: Chemical ChemComp-GNG / 2'-DEOXY-GUANOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 622 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.01M K-HEPES, 0.0119 M cobalt(III) hexammine, 22% PEG 2000, 0.66M ammonium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1K-HEPES11
2cobalt(III) hexammine11
3PEG 200011
4ammonium acetate11
5H2O11
6K-HEPES12
7cobalt(III) hexammine12
8PEG 200012
9ammonium acetate12
10H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 12, 2007
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→19.5 Å / Num. all: 31039 / Num. obs: 29177 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 3.56 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 8.4
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.57 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2822 / % possible all: 91.4

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Processing

Software
NameVersionClassification
CNS1.2refinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 1U8D

1u8d
PDB Unreleased entry


Resolution: 1.85→19.5 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 518064.88 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2894 10 %RANDOM
Rwork0.2 ---
all0.208 31039 --
obs0.205 29005 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.7773 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 34.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.69 Å20.8 Å2-0.28 Å2
2---0.76 Å22.34 Å2
3---2.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.85→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2853 123 622 3598
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d17.9
X-RAY DIFFRACTIONc_improper_angle_d2.58
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 482 10.4 %
Rwork0.264 4165 -
obs--89.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1water_rep.paramwater.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3acetate.paramacetate.top
X-RAY DIFFRACTION4gng.paramgng.top
X-RAY DIFFRACTION5cohex4.paramcohex4.top

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