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

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Basic information

Entry
Database: PDB / ID: 5hbx
TitleRNA primer-template complex with 2-methylimidazole-activated monomer analogue-2 binding sites
ComponentsRNA (5'-R(*(LCC)P*(LCC)P*(LCA)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*U)-3')
KeywordsRNA
Function / homologyChem-PZG / RNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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*(LCC)P*(LCA)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*U)-3')
B: RNA (5'-R(*(LCC)P*(LCC)P*(LCA)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*U)-3')
C: RNA (5'-R(*(LCC)P*(LCC)P*(LCA)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*U)-3')
D: RNA (5'-R(*(LCC)P*(LCC)P*(LCA)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,35412
Polymers17,9354
Non-polymers3,4188
Water1,63991
1
A: RNA (5'-R(*(LCC)P*(LCC)P*(LCA)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*U)-3')
B: RNA (5'-R(*(LCC)P*(LCC)P*(LCA)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6776
Polymers8,9682
Non-polymers1,7094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint4 kcal/mol
Surface area5910 Å2
MethodPISA
2
C: RNA (5'-R(*(LCC)P*(LCC)P*(LCA)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*U)-3')
D: RNA (5'-R(*(LCC)P*(LCC)P*(LCA)P*(LCG)P*AP*CP*UP*UP*AP*AP*GP*UP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6776
Polymers8,9682
Non-polymers1,7094
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint4 kcal/mol
Surface area5910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.545, 43.545, 83.996
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-203-

HOH

21A-213-

HOH

31A-220-

HOH

41A-221-

HOH

51B-204-

HOH

61B-205-

HOH

71B-222-

HOH

81C-205-

HOH

91C-216-

HOH

101C-223-

HOH

111D-204-

HOH

121D-211-

HOH

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Components

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


Mass: 4483.762 Da / Num. of mol.: 4 / 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.: 8 / Source method: obtained synthetically / Formula: C14H18N7O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.39 Å3/Da / Density % sol: 52.02 % / Description: a diamond shape crystal
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Ammonium acetate, Magnesium chloride hexahydrate,0.05 M TRIS hydrochloride pH 7.5,10% v/v (+/-)-2-Methyl-2,4-pentanediol
PH range: 7.5

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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: 1.7→50 Å / Num. all: 19566 / Num. obs: 19566 / % possible obs: 99.9 % / Observed criterion σ(F): 0.05 / Observed criterion σ(I): 0.05 / Redundancy: 7.4 % / Rmerge(I) obs: 0.128 / Net I/av σ(I): 14.6 / Net I/σ(I): 14.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.64 / % possible all: 100

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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: 5DHC

5dhc


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.567 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0.05 / ESU R: 0.129 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24899 1103 5.6 %RANDOM
Rwork0.21292 ---
obs0.21478 18463 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.324 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1188 232 91 1511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0181576
X-RAY DIFFRACTIONr_bond_other_d0.0410.024708
X-RAY DIFFRACTIONr_angle_refined_deg2.772.032432
X-RAY DIFFRACTIONr_angle_other_deg3.8693.2691700
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_restr0.1220.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.021816
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022296
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_it3.733.031576
X-RAY DIFFRACTIONr_scbond_other3.7293.0351577
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7284.5292433
X-RAY DIFFRACTIONr_long_range_B_refined8.67528.2762244
X-RAY DIFFRACTIONr_long_range_B_other8.69528.3032231
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.702→1.746 Å
RfactorNum. reflection% reflection
Rfree0.223 109 -
Rwork0.223 1361 -
obs--99.19 %

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