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- PDB-4pco: Crystal structure of double-stranded RNA with four terminal GU wo... -

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Basic information

Entry
Database: PDB / ID: 4pco
TitleCrystal structure of double-stranded RNA with four terminal GU wobble base pairs
ComponentsRNA (5'-D(*GP*GP*UP*GP*GP*CP*UP*GP*UP*U)-3')
KeywordsRNA / GU wobble base pair motif
Function / homologyCOBALT HEXAMMINE(III) / RNA
Function and homology information
Biological speciesEndothia gyrosa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.32 Å
Model detailsoverwound RNA; cobalt hexamine binding, chloride binding
AuthorsMooers, B.H.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI088011 United States
CitationJournal: J.Phys.Chem.B / Year: 2015
Title: Structures and Energetics of Four Adjacent GU Pairs That Stabilize an RNA Helix.
Authors: Gu, X. / Mooers, B.H. / Thomas, L.M. / Malone, J. / Harris, S. / Schroeder, S.J.
History
DepositionApr 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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'-D(*GP*GP*UP*GP*GP*CP*UP*GP*UP*U)-3')
B: RNA (5'-D(*GP*GP*UP*GP*GP*CP*UP*GP*UP*U)-3')
C: RNA (5'-D(*GP*GP*UP*GP*GP*CP*UP*GP*UP*U)-3')
D: RNA (5'-D(*GP*GP*UP*GP*GP*CP*UP*GP*UP*U)-3')
E: RNA (5'-D(*GP*GP*UP*GP*GP*CP*UP*GP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,09420
Polymers16,0555
Non-polymers2,04015
Water3,423190
1
A: RNA (5'-D(*GP*GP*UP*GP*GP*CP*UP*GP*UP*U)-3')
B: RNA (5'-D(*GP*GP*UP*GP*GP*CP*UP*GP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,49511
Polymers6,4222
Non-polymers1,0739
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-46 kcal/mol
Surface area3530 Å2
MethodPISA
2
C: RNA (5'-D(*GP*GP*UP*GP*GP*CP*UP*GP*UP*U)-3')
D: RNA (5'-D(*GP*GP*UP*GP*GP*CP*UP*GP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0666
Polymers6,4222
Non-polymers6444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-27 kcal/mol
Surface area3820 Å2
MethodPISA
3
E: RNA (5'-D(*GP*GP*UP*GP*GP*CP*UP*GP*UP*U)-3')
hetero molecules

E: RNA (5'-D(*GP*GP*UP*GP*GP*CP*UP*GP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0666
Polymers6,4222
Non-polymers6444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2520 Å2
ΔGint-25 kcal/mol
Surface area3300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.616, 43.224, 83.256
Angle α, β, γ (deg.)90.00, 102.48, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-216-

HOH

21E-222-

HOH

31E-227-

HOH

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Components

#1: RNA chain
RNA (5'-D(*GP*GP*UP*GP*GP*CP*UP*GP*UP*U)-3') / GU rich dsRNA


Mass: 3210.916 Da / Num. of mol.: 5 / Source method: obtained synthetically / Details: phsophoramidite synthesis / Source: (synth.) Endothia gyrosa (fungus)
#2: Chemical
ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CoH18N6
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.6 % / Description: orange plates
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 15 mg/mL RNA, 26.2% (v/v) 2-methyl-2,4-pentanediol (MPD), 0.04 M lithium chloride, 0.03 M cobalt hexamine chloride, 0.04 M sodium cacodylate, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9795, 1.3624, 1.6053, 1.6068
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2013 / Details: Rh coated flat mirrors
RadiationMonochromator: Side scattering I-beam bent single crystal, asymmetric cut 4.9650 deg
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21.36241
31.60531
41.60681
ReflectionResolution: 1.32→81.289 Å / Num. all: 29968 / Num. obs: 29968 / % possible obs: 100 % / Redundancy: 7.9 % / Biso Wilson estimate: 11.98 Å2 / Rpim(I) all: 0.023 / Rrim(I) all: 0.07 / Rsym value: 0.06 / Net I/av σ(I): 5.063 / Net I/σ(I): 18.2 / Num. measured all: 236794
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.32-1.397.20.6671.23119543250.2890.6672.7100
1.39-1.487.20.4161.93004141510.1810.4164.2100
1.48-1.587.30.2463.12827338840.1070.2466.8100
1.58-1.77.30.135.62599235770.0570.1311.7100
1.7-1.877.30.0957.62438133440.0420.09516100
1.87-2.097.30.0719.72188530070.0320.07121.5100
2.09-2.417.80.06110.62081326710.0260.06128.6100
2.41-2.9510.80.0549.62432722480.0190.05440.5100
2.95-4.17110.0410.71948117680.0140.0457.8100
4.17-27.52110.50.0458.7104069930.0170.04561.499.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PHENIX1.9_1678refinement
SHELXphasing
SHELXphasing
PDB_EXTRACT3.14data extraction
Cootmodel building
Blu-Icedata collection
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.32→27.521 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0.88 / Phase error: 19.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1835 2957 5.05 %Random selection
Rwork0.1552 ---
obs0.1567 29968 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.32→27.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1060 87 190 1337
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051399
X-RAY DIFFRACTIONf_angle_d1.0382251
X-RAY DIFFRACTIONf_dihedral_angle_d7.186651
X-RAY DIFFRACTIONf_chiral_restr0.033274
X-RAY DIFFRACTIONf_plane_restr0.01156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.34170.24221590.24452705X-RAY DIFFRACTION100
1.3417-1.36480.25021320.24192607X-RAY DIFFRACTION100
1.3648-1.38960.27851300.22152600X-RAY DIFFRACTION100
1.3896-1.41630.22051440.19852731X-RAY DIFFRACTION100
1.4163-1.44530.20461350.18932605X-RAY DIFFRACTION100
1.4453-1.47670.25631420.18292660X-RAY DIFFRACTION100
1.4767-1.5110.18191420.17712644X-RAY DIFFRACTION100
1.511-1.54880.2141180.16472638X-RAY DIFFRACTION100
1.5488-1.59070.22451280.15032727X-RAY DIFFRACTION100
1.5907-1.63750.19251290.14492597X-RAY DIFFRACTION100
1.6375-1.69030.17311370.13932663X-RAY DIFFRACTION100
1.6903-1.75070.17531500.13792656X-RAY DIFFRACTION100
1.7507-1.82080.19341410.14722601X-RAY DIFFRACTION100
1.8208-1.90370.21731540.14742677X-RAY DIFFRACTION100
1.9037-2.0040.18571330.14462662X-RAY DIFFRACTION100
2.004-2.12950.20381090.14692653X-RAY DIFFRACTION100
2.1295-2.29390.17221310.15152673X-RAY DIFFRACTION100
2.2939-2.52460.19011690.16352596X-RAY DIFFRACTION100
2.5246-2.88950.18681690.16582638X-RAY DIFFRACTION100
2.8895-3.63920.16891410.13912648X-RAY DIFFRACTION100
3.6392-27.52740.14511640.14412623X-RAY DIFFRACTION100

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