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- PDB-6bmd: RNA hairpin containing GpppG-oligo to mimic intermediate formed b... -

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Basic information

Entry
Database: PDB / ID: 6bmd
TitleRNA hairpin containing GpppG-oligo to mimic intermediate formed by activated monomer and activated downstream helper
Components
  • RNA (5'-D(*(GP3))-R(P*CP*AP*CP*CP*UP*CP*A)-3')
  • RNA (5'-R(P*GP*AP*GP*GP*UP*GP*(LCC)P*(LCC)P*GP*AP*GP*CP*GP*CP*GP*AP*AP*AP*GP*CP*GP*CP*UP*C)-3')
KeywordsRNA / GpppG / helper / intermediate
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsZhang, W. / Szostak, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Howar United States
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
DepositionNov 14, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(P*GP*AP*GP*GP*UP*GP*(LCC)P*(LCC)P*GP*AP*GP*CP*GP*CP*GP*AP*AP*AP*GP*CP*GP*CP*UP*C)-3')
B: RNA (5'-D(*(GP3))-R(P*CP*AP*CP*CP*UP*CP*A)-3')
C: RNA (5'-R(P*GP*AP*GP*GP*UP*GP*(LCC)P*(LCC)P*GP*AP*GP*CP*GP*CP*GP*AP*AP*AP*GP*CP*GP*CP*UP*C)-3')
D: RNA (5'-D(*(GP3))-R(P*CP*AP*CP*CP*UP*CP*A)-3')
E: RNA (5'-R(P*GP*AP*GP*GP*UP*GP*(LCC)P*(LCC)P*GP*AP*GP*CP*GP*CP*GP*AP*AP*AP*GP*CP*GP*CP*UP*C)-3')
F: RNA (5'-D(*(GP3))-R(P*CP*AP*CP*CP*UP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)32,2946
Polymers32,2946
Non-polymers00
Water66737
1
A: RNA (5'-R(P*GP*AP*GP*GP*UP*GP*(LCC)P*(LCC)P*GP*AP*GP*CP*GP*CP*GP*AP*AP*AP*GP*CP*GP*CP*UP*C)-3')
B: RNA (5'-D(*(GP3))-R(P*CP*AP*CP*CP*UP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)10,7652
Polymers10,7652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-0 kcal/mol
Surface area6150 Å2
MethodPISA
2
C: RNA (5'-R(P*GP*AP*GP*GP*UP*GP*(LCC)P*(LCC)P*GP*AP*GP*CP*GP*CP*GP*AP*AP*AP*GP*CP*GP*CP*UP*C)-3')
D: RNA (5'-D(*(GP3))-R(P*CP*AP*CP*CP*UP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)10,7652
Polymers10,7652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint1 kcal/mol
Surface area6140 Å2
MethodPISA
3
E: RNA (5'-R(P*GP*AP*GP*GP*UP*GP*(LCC)P*(LCC)P*GP*AP*GP*CP*GP*CP*GP*AP*AP*AP*GP*CP*GP*CP*UP*C)-3')
F: RNA (5'-D(*(GP3))-R(P*CP*AP*CP*CP*UP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)10,7652
Polymers10,7652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint1 kcal/mol
Surface area6150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.392, 63.759, 65.840
Angle α, β, γ (deg.)90.00, 122.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain RNA (5'-R(P*GP*AP*GP*GP*UP*GP*(LCC)P*(LCC)P*GP*AP*GP*CP*GP*CP*GP*AP*AP*AP*GP*CP*GP*CP*UP*C)-3')


Mass: 7853.808 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: RNA chain RNA (5'-D(*(GP3))-R(P*CP*AP*CP*CP*UP*CP*A)-3')


Mass: 2910.738 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 50 mM MgCl2, 3 M ammonia sulfate, 100 mM HEPES 7.5

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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 165 mm / Detector: CCD / Date: Oct 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 7315 / % possible obs: 95.9 % / Redundancy: 4.8 % / CC1/2: 0.97 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.094 / Rrim(I) all: 0.213 / Rsym value: 0.144 / Χ2: 0.654 / Net I/σ(I): 5.8
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 557 / CC1/2: 0.904 / Rpim(I) all: 0.198 / Rrim(I) all: 0.429 / Rsym value: 0.334 / Χ2: 0.571 / % possible all: 74.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UZ6

5uz6


Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.914 / SU B: 18.539 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R Free: 0.402 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2305 392 5.4 %RANDOM
Rwork0.18352 ---
obs0.1861 6922 95.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.407 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å2-0.05 Å2
2--0.12 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 2157 0 37 2194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132400
X-RAY DIFFRACTIONr_bond_other_d0.0190.021981
X-RAY DIFFRACTIONr_angle_refined_deg2.061.5043723
X-RAY DIFFRACTIONr_angle_other_deg2.3973.0732385
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_restr0.1750.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021203
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02513
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_it1.7852.8532399
X-RAY DIFFRACTIONr_scbond_other1.7852.8532400
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7074.2783723
X-RAY DIFFRACTIONr_long_range_B_refined3.86227.6123458
X-RAY DIFFRACTIONr_long_range_B_other3.86127.6093459
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 22 -
Rwork0.264 371 -
obs--71.2 %

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