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- PDB-6az4: RNA hairpin complex with guanosine dinucleotide ligand G(5')ppp(5')G -

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Basic information

Entry
Database: PDB / ID: 6az4
TitleRNA hairpin complex with guanosine dinucleotide ligand G(5')ppp(5')G
Components
  • RNA (32-MER)
  • RNA (5'-R(*CP*AP*GP*CP*AP*GP*CP*AP*G)-3')
KeywordsRNA
Function / homologyDIGUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsZhang, W. / Szostak, J.W.
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide.
Authors: Zhang, W. / Tam, C.P. / Zhou, L. / Oh, S.S. / Wang, J. / Szostak, J.W.
History
DepositionSep 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (32-MER)
B: RNA (5'-R(*CP*AP*GP*CP*AP*GP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9393
Polymers13,1512
Non-polymers7881
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint1 kcal/mol
Surface area7510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.388, 79.388, 73.652
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: RNA chain RNA (32-MER)


Mass: 10257.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (5'-R(*CP*AP*GP*CP*AP*GP*CP*AP*G)-3')


Mass: 2893.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GP3 / DIGUANOSINE-5'-TRIPHOSPHATE


Mass: 788.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N10O18P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 4.3 Å3/Da / Density % sol: 71.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.05 M Magnesium chloride, 0.1 M Sodium cacodylate trihydrate pH 6.5, 1.4 M Sodium acetate trihydrate

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Data collection

DiffractionMean temperature: 99 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Sep 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.98→50 Å / Num. obs: 4712 / % possible obs: 91.6 % / Redundancy: 4.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.133 / Χ2: 0.9 / Net I/σ(I): 9.24
Reflection shellResolution: 2.98→3.09 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.698 / Mean I/σ(I) obs: 1.64 / Num. unique obs: 476 / CC1/2: 0.978 / Χ2: 0.591 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000v1.0data reduction
HKL-2000v1.0data scaling
REFMAC5.8.0158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FNJ

4fnj


Resolution: 2.98→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 13.839 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.617 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2325 247 5.2 %RANDOM
Rwork0.18053 ---
obs0.18206 4464 91.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.195 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 2.98→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 870 51 2 923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121028
X-RAY DIFFRACTIONr_bond_other_d0.0050.02420
X-RAY DIFFRACTIONr_angle_refined_deg2.1851.3751600
X-RAY DIFFRACTIONr_angle_other_deg1.8183.0251020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.2420.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02511
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02222
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.2187.7391025
X-RAY DIFFRACTIONr_scbond_other6.2167.7391026
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.96911.61599
X-RAY DIFFRACTIONr_long_range_B_refined10.78375.741443
X-RAY DIFFRACTIONr_long_range_B_other10.77975.7241444
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.983→3.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 19 -
Rwork0.33 323 -
obs--92.93 %

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