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- PDB-5hbw: RNA primer-template complex with 2-methylimidazole-activated mono... -

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Basic information

Entry
Database: PDB / ID: 5hbw
TitleRNA primer-template complex with 2-methylimidazole-activated monomer analogue
ComponentsRNA (5'-R(*(LCC)P*(TLN)P*(LCG)P*UP*AP*CP*A)-3')
KeywordsRNA
Function / homologyChem-PZG / RNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhang, W. / Tam, C.P. / Szostak, J.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: ACS Cent Sci / Year: 2016
Title: Unusual Base-Pairing Interactions in Monomer-Template Complexes.
Authors: Zhang, W. / Tam, C.P. / Wang, J. / Szostak, J.W.
History
DepositionJan 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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(*(LCC)P*(TLN)P*(LCG)P*UP*AP*CP*A)-3')
B: RNA (5'-R(*(LCC)P*(TLN)P*(LCG)P*UP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3454
Polymers4,4912
Non-polymers8552
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint15 kcal/mol
Surface area3150 Å2
Unit cell
Length a, b, c (Å)28.076, 39.747, 42.593
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: RNA chain RNA (5'-R(*(LCC)P*(TLN)P*(LCG)P*UP*AP*CP*A)-3')


Mass: 2245.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-PZG / [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-(3-methyl-1~{H}-pyrazol-4-yl)phosphinic acid


Type: DNA linking / Mass: 427.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18N7O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.51 % / Description: needle
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: (+/-)-2-Methyl-2,4-pentanediol, Sodium cacodylate trihydrate, Spermine tetrahydrochloride, Sodium chloride, Potassium chloride, Magnesium chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.987 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 18, 2015
RadiationMonochromator: none / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 4036 / Num. obs: 4036 / % possible obs: 99.7 % / Observed criterion σ(F): 0.05 / Observed criterion σ(I): 0.05 / Redundancy: 6.1 % / Rmerge(I) obs: 0.053 / Net I/av σ(I): 24.8 / Net I/σ(I): 24.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 3.3 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DNS

1dns


Resolution: 1.9→23.44 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.969 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25416 195 4.8 %RANDOM
Rwork0.21696 ---
obs0.21857 3841 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2--0.03 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.9→23.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 298 58 3 359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.019394
X-RAY DIFFRACTIONr_bond_other_d0.0380.025184
X-RAY DIFFRACTIONr_angle_refined_deg3.4852.234606
X-RAY DIFFRACTIONr_angle_other_deg4.5883.336440
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_restr0.1660.270
X-RAY DIFFRACTIONr_gen_planes_refined0.020.021206
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02272
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_it3.583.547394
X-RAY DIFFRACTIONr_scbond_other3.5753.554395
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8775.333607
X-RAY DIFFRACTIONr_long_range_B_refined5.50133.694572
X-RAY DIFFRACTIONr_long_range_B_other5.49633.76573
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.898→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 20 -
Rwork0.291 250 -
obs--96.43 %

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