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- PDB-7ucr: Joint X-ray/neutron structure of the Sarcin-Ricin loop RNA -

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Basic information

Entry
Database: PDB / ID: 7ucr
TitleJoint X-ray/neutron structure of the Sarcin-Ricin loop RNA
ComponentsSarcin-Ricin loop RNA
KeywordsRNA / Sarcin-Ricin loop
Function / homologyDEUTERATED WATER / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsHarp, J.M. / Egli, M.E. / Pallan, P.S. / Coates, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Cryo neutron crystallography demonstrates influence of RNA 2'-OH orientation on conformation, sugar pucker and water structure.
Authors: Harp, J.M. / Lybrand, T.P. / Pallan, P.S. / Coates, L. / Sullivan, B. / Egli, M.
History
DepositionMar 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 3, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sarcin-Ricin loop RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8402
Polymers8,7441
Non-polymers961
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.495, 29.495, 76.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2

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Components

#1: RNA chain Sarcin-Ricin loop RNA


Mass: 8744.255 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: D2O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.37 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.233 mM RNA, 1.0 M ammonium sulfate, 2 mM magnesium chloride, 2 mM manganese chloride, 16.5 mM -3-(N-morpholino)propanesulfonic acid.

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
LIQUID ANODEExcillum MetalJet D2 70 kV11.342
SPALLATION SOURCEORNL Spallation Neutron Source MANDI22.0-4.0
Detector
TypeIDDetectorDate
Bruker PHOTON III1PIXELFeb 14, 2020
ORNL ANGER CAMERA2AREA DETECTORJan 29, 2020
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1multilayer, confocalSINGLE WAVELENGTHMx-ray1
2LAUELneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.3421
221
341
Reflection

Biso Wilson estimate: 8.3 Å2 / Entry-ID: 7UCR

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rmerge(I) obsDiffraction-IDNet I/σ(I)
0.998-16.053532699.6713.680.9990.055121.66
2.25-12.34288792.323.40.8860.21229.8
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID
0.998-1.0330.41234610.8491
2.25-2.330.2997710.32

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHENIX1.18.2_3874phasing
Refinement

SU ML: 0.1008 / Cross valid method: FREE R-VALUE / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 23.1382 / Shrinkage radii: 0.5 Å / VDW probe radii: 0.9 Å / Starting model: 3DVZ

3dvz

/ Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDBiso mean (Å2)Rfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection RworkNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)Details
1-16.05X-RAY DIFFRACTION17.210.19650.17850.1812348366289352724.9999.4211.34The G61 residue in the structure is in fact a G46 residue with a monothiophosphate. Due to the extreme difference in scattering by the sulfur atom for X-rays versus neutrons, modeling of the monothiophosphate was not appropriate and the sulfur atom was left out of the final deposition.
2.25-12.34NEUTRON DIFFRACTION0.29870.2543288692.322
Refinement stepCycle: LAST / Resolution: 1→16.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 579 5 80 664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01151273
X-RAY DIFFRACTIONf_angle_d1.61112043
X-RAY DIFFRACTIONf_chiral_restr0.1076146
X-RAY DIFFRACTIONf_plane_restr0.0129103
X-RAY DIFFRACTIONf_dihedral_angle_d23.333453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.010.28721330.28162486X-RAY DIFFRACTION91.51
1.01-1.030.28751420.25262621X-RAY DIFFRACTION99.93
1.03-1.040.26211380.242683X-RAY DIFFRACTION99.96
1.04-1.060.26741360.23672666X-RAY DIFFRACTION100
1.06-1.070.23421420.21812657X-RAY DIFFRACTION99.96
1.07-1.090.22261330.21012670X-RAY DIFFRACTION100
1.09-1.110.23981400.20692626X-RAY DIFFRACTION99.89
1.11-1.130.22411500.20672736X-RAY DIFFRACTION99.97
1.13-1.160.24611380.19732644X-RAY DIFFRACTION99.93
1.16-1.180.20561460.19842652X-RAY DIFFRACTION99.93
1.18-1.210.17581360.19622599X-RAY DIFFRACTION99.82
1.21-1.240.23111440.18812721X-RAY DIFFRACTION99.83
1.24-1.270.23391440.18042616X-RAY DIFFRACTION99.93
1.27-1.310.18311360.1782704X-RAY DIFFRACTION99.93
1.31-1.350.18271400.18232652X-RAY DIFFRACTION99.96
1.35-1.40.19921340.18322714X-RAY DIFFRACTION99.96
1.4-1.460.19981360.18562631X-RAY DIFFRACTION100
1.46-1.520.16361400.17352650X-RAY DIFFRACTION99.86
1.52-1.610.16991360.18192698X-RAY DIFFRACTION99.93
1.61-1.710.14161420.14962619X-RAY DIFFRACTION99.86
1.71-1.840.21451380.16112699X-RAY DIFFRACTION99.82
1.84-2.020.22361320.17532651X-RAY DIFFRACTION99.86
2.02-2.310.20341480.20052665X-RAY DIFFRACTION99.86
2.31-2.910.21941340.20262671X-RAY DIFFRACTION99.96
2.91-16.050.1581450.14012558X-RAY DIFFRACTION96.29

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