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

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Basic information

Entry
Database: PDB / ID: 5hby
TitleRNA primer-template complex with 2-methylimidazole-activated monomer analogue-3 binding sites
ComponentsRNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*C)-3')
KeywordsRNA
Function / homologyChem-PZG / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.18 Å
AuthorsZhang, W. / Tam, C.P. / Wang, J. / 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 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,0474
Polymers4,1681
Non-polymers8793
Water1,20767
1
A: RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*C)-3')
hetero molecules

A: RNA (5'-R(*(LCC)P*(LCC)P*(LCC)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0938
Polymers8,3352
Non-polymers1,7586
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2080 Å2
ΔGint-5 kcal/mol
Surface area6480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.873, 31.987, 33.426
Angle α, β, γ (deg.)90.00, 122.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-254-

HOH

21A-267-

HOH

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Components

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


Mass: 4167.598 Da / Num. of mol.: 1 / 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.6 Å3/Da / Density % sol: 50.69 % / Description: boat shape crystal
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: Potassium thiocyanate,magnesium chloride,30% w/v Polyethylene glycol monomethyl ether 2,000
PH range: 7.3

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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: 1.18→50 Å / Num. all: 12711 / Num. obs: 12711 / % possible obs: 93.6 % / Observed criterion σ(F): 0.05 / Observed criterion σ(I): 0.05 / Redundancy: 3.7 % / Rmerge(I) obs: 0.047 / Net I/av σ(I): 26.5 / Net I/σ(I): 26.5
Reflection shellResolution: 1.18→1.22 Å / Redundancy: 2 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 1.8 / % possible all: 54.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.18→50 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.571 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0.05 / ESU R: 0.037 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16566 620 4.9 %RANDOM
Rwork0.15321 ---
obs0.15385 12091 93.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.288 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.18→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 276 59 67 402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0350.018370
X-RAY DIFFRACTIONr_bond_other_d0.050.024170
X-RAY DIFFRACTIONr_angle_refined_deg3.0362.058571
X-RAY DIFFRACTIONr_angle_other_deg3.7053.285406
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_restr0.7090.265
X-RAY DIFFRACTIONr_gen_planes_refined0.0380.021194
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02270
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_it1.1211.258369
X-RAY DIFFRACTIONr_scbond_other1.1211.26370
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4881.898572
X-RAY DIFFRACTIONr_long_range_B_refined2.45513.114570
X-RAY DIFFRACTIONr_long_range_B_other2.12912.763538
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.181→1.211 Å
RfactorNum. reflection% reflection
Rfree0.258 29 -
Rwork0.248 470 -
obs--50.1 %

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