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- PDB-4o41: Amide linked RNA -

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Basic information

Entry
Database: PDB / ID: 4o41
TitleAmide linked RNA
ComponentsAMIDE LINKED RNA
KeywordsRNA / Modified RNA / RNA structure / amide RNA / amide internucleoside linkage / modified nucleoside
Function / homologySTRONTIUM ION / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsPallan, P.S. / Egli, M.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Amides are excellent mimics of phosphate internucleoside linkages and are well tolerated in short interfering RNAs.
Authors: Mutisya, D. / Selvam, C. / Lunstad, B.D. / Pallan, P.S. / Haas, A. / Leake, D. / Egli, M. / Rozners, E.
History
DepositionDec 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Refinement description
Revision 1.2Feb 28, 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 / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AMIDE LINKED RNA
B: AMIDE LINKED RNA
C: AMIDE LINKED RNA
D: AMIDE LINKED RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4616
Polymers16,2864
Non-polymers1752
Water5,116284
1
A: AMIDE LINKED RNA
B: AMIDE LINKED RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3184
Polymers8,1432
Non-polymers1752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-59 kcal/mol
Surface area4880 Å2
MethodPISA
2
C: AMIDE LINKED RNA
D: AMIDE LINKED RNA


Theoretical massNumber of molelcules
Total (without water)8,1432
Polymers8,1432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-6 kcal/mol
Surface area4620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)22.360, 34.330, 43.300
Angle α, β, γ (deg.)110.03, 94.24, 95.83
Int Tables number1
Space group name H-MP1

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Components

#1: RNA chain
AMIDE LINKED RNA


Mass: 4071.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Chemically synthesized modified Ribo Nucleic Acid
#2: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sr
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Compound detailsURU represents the amide linked residue

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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: 1.89 Å3/Da / Density % sol: 35.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20 mM sodium cacodylate, 45 mM strontium chloride, 10 mM magnesium chloride, 6 mM spermine tetrahydrochloride and 5% 2-methyl-2,4-pentanediol [MPD (v/v)], pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.7686 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 17, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7686 Å / Relative weight: 1
ReflectionResolution: 1.2→28 Å / Num. all: 37491 / Num. obs: 35934 / % possible obs: 95.8 % / Observed criterion σ(I): 5 / Redundancy: 7.7 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 14.66
Reflection shellResolution: 1.2→1.4 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 6.21 / Num. unique all: 13205 / % possible all: 94.8

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Processing

Software
NameVersionClassification
MD2diffractometer software from EMBL (with LS-CAT developed extensionsdata collection
Singlewavelength anomalous dispersionmodel building
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
Singlewavelength anomalous dispersionphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→28 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.212 1795 RANDOM
Rwork0.147 --
all-37491 -
obs-35886 -
Refinement stepCycle: LAST / Resolution: 1.2→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1029 2 284 1315
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.0327

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