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- PDB-4jrd: Crystal structure of the parallel double-stranded helix of poly(A) RNA -

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Basic information

Entry
Database: PDB / ID: 4jrd
TitleCrystal structure of the parallel double-stranded helix of poly(A) RNA
ComponentsRNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
KeywordsRNA / PARALLEL DOUBLE HELIX / POLY(A) / MRNA / PABP / Poly(A) motif
Function / homologyAMMONIUM ION / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1 Å
AuthorsSafaee, N. / Noronha, A.M. / Kozlov, G. / Rodionov, D. / Wilds, C.J. / Sheldrick, G.M. / Gehring, K.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Structure of the parallel duplex of poly(A) RNA: evaluation of a 50 year-old prediction.
Authors: Safaee, N. / Noronha, A.M. / Rodionov, D. / Kozlov, G. / Wilds, C.J. / Sheldrick, G.M. / Gehring, K.
History
DepositionMar 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
B: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,47720
Polymers7,1532
Non-polymers32518
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)22.800, 22.800, 163.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-225-

HOH

21B-217-

HOH

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Components

#1: RNA chain RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 3576.306 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: H4N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

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Sample preparation

CrystalDensity Matthews: 1.49 Å3/Da / Density % sol: 17.29 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: RNA WATER SOLUTION PLUS BUFFER (10 MM HEPES, 50 MM NACL, 0.5 MM TCEP, PH 7.0) MIXED 1:1 V/V WITH 2 M (NH4)2SO4 + 0.2 M NH4NO3 AND EQUILIBRATED AGAINST 2 M (NH4)2SO4 + 0.2 M NH4NO3, VAPOR ...Details: RNA WATER SOLUTION PLUS BUFFER (10 MM HEPES, 50 MM NACL, 0.5 MM TCEP, PH 7.0) MIXED 1:1 V/V WITH 2 M (NH4)2SO4 + 0.2 M NH4NO3 AND EQUILIBRATED AGAINST 2 M (NH4)2SO4 + 0.2 M NH4NO3, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
41001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONCLSI 08ID-110.977
SYNCHROTRONCHESS A120.987
SYNCHROTRONCHESS A130.987
SYNCHROTRONCHESS A140.987
Detector
TypeIDDetectorDateDetails
MARMOSAIC 300 mm CCD1CCDMay 29, 2010FOCUSING MIRRORS
ADSC QUANTUM 2102CCDOct 21, 2010FOCUSING MIRRORS
ADSC QUANTUM 2103CCDOct 21, 2010FOCUSING MIRRORS
ADSC QUANTUM 2104CCDOct 21, 2010FOCUSING MIRRORS
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI 111 DOUBLESINGLE WAVELENGTHMx-ray1
2Horizontal focusing 5.05 asymmetric cut Si(111)SINGLE WAVELENGTHMx-ray1
3Horizontal focusing 5.05 asymmetric cut Si(111)SINGLE WAVELENGTHMx-ray1
4Horizontal focusing 5.05 asymmetric cut Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9771
20.9871
ReflectionResolution: 1→41 Å / Num. all: 23042 / Num. obs: 22972 / % possible obs: 92.6 % / Observed criterion σ(F): 4 / Observed criterion σ(I): -3 / Redundancy: 2.73 % / Rmerge(I) obs: 0.0944 / Net I/σ(I): 34.35
Reflection shellResolution: 1→1.1 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.1419 / Mean I/σ(I) obs: 4.72 / % possible all: 73.1

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Processing

Software
NameClassification
MxDCdata collection
SHELXDphasing
SHELXLrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1→41 Å / Num. parameters: 5165 / Num. restraintsaints: 6773 / Cross valid method: FREE R / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.158 1152 5.01 %RANDOM
Rwork0.118 ---
obs0.126 22972 92.6 %-
all-23042 --
Solvent computationSolvent model: BABINET
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 242 / Occupancy sum non hydrogen: 571
Refinement stepCycle: LAST / Resolution: 1→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 478 18 76 572
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_from_restr_planes0.038
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.021
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.015
X-RAY DIFFRACTIONs_approx_iso_adps0.1

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