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- PDB-5da6: Atomic resolution crystal structure of double-stranded RNA 32 bas... -

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Basic information

Entry
Database: PDB / ID: 5da6
TitleAtomic resolution crystal structure of double-stranded RNA 32 base pairs long determined from random starting phases angles in the presence of pseudo translational symmetry using the direct methods program SIR2014.
ComponentsRNA (32-MER)
KeywordsRNA / RNA editing substrate / double-stranded RNA / direct methods structure determination / pseudo translational symmetry
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.05 Å
AuthorsMooers, B.H.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI088011 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20 GM103640 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Direct-methods structure determination of a trypanosome RNA-editing substrate fragment with translational pseudosymmetry.
Authors: Mooers, B.H.
History
DepositionAug 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Mar 6, 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
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_alt_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_alt_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_ptnr1_label_alt_id / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2562
Polymers10,2171
Non-polymers391
Water4,252236
1
A: RNA (32-MER)
hetero molecules

A: RNA (32-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5124
Polymers20,4342
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area2920 Å2
ΔGint-29 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.890, 42.890, 266.936
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-101-

K

21A-256-

HOH

31A-289-

HOH

41A-300-

HOH

51A-323-

HOH

61A-325-

HOH

71A-344-

HOH

81A-352-

HOH

91A-362-

HOH

101A-366-

HOH

111A-368-

HOH

121A-375-

HOH

131A-409-

HOH

141A-412-

HOH

151A-418-

HOH

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Components

#1: RNA chain RNA (32-MER)


Mass: 10216.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: AGAGAAGAAAGGGAAAUUUUUUUUUUUUUUUU / Source: (synth.) Trypanosoma brucei (eukaryote)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Lithium sulfate, magnesium chloride, cacodylate / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.05→36.79 Å / Num. obs: 44942 / % possible obs: 99.6 % / Redundancy: 4 % / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 20.1
Reflection shellResolution: 1.05→1.11 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 3.8 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.10_2142refinement
iMOSFLMdata reduction
SCALAdata scaling
Sir2014phasing
Coot0.82premodel building
Blu-Icedata collection
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.05→36.789 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1568 2337 5.2 %
Rwork0.1286 --
obs0.1301 44941 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.05→36.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 675 1 236 912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005853
X-RAY DIFFRACTIONf_angle_d1.0381328
X-RAY DIFFRACTIONf_dihedral_angle_d6.261427
X-RAY DIFFRACTIONf_chiral_restr0.039178
X-RAY DIFFRACTIONf_plane_restr0.01836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.05-1.07140.24321530.22622437X-RAY DIFFRACTION99
1.0714-1.09470.19111170.18162504X-RAY DIFFRACTION100
1.0947-1.12020.19571220.1692445X-RAY DIFFRACTION99
1.1202-1.14820.17221300.16952476X-RAY DIFFRACTION100
1.1482-1.17930.1461250.13952483X-RAY DIFFRACTION100
1.1793-1.2140.14371520.11982464X-RAY DIFFRACTION100
1.214-1.25320.14851430.10812452X-RAY DIFFRACTION100
1.2532-1.29790.11471400.11172514X-RAY DIFFRACTION100
1.2979-1.34990.14961140.11312507X-RAY DIFFRACTION100
1.3499-1.41140.13291290.11782488X-RAY DIFFRACTION100
1.4114-1.48580.14331310.112533X-RAY DIFFRACTION100
1.4858-1.57890.12961540.10712485X-RAY DIFFRACTION100
1.5789-1.70080.12511560.10292474X-RAY DIFFRACTION99
1.7008-1.87190.12581320.10432534X-RAY DIFFRACTION100
1.8719-2.14270.14471450.12272559X-RAY DIFFRACTION100
2.1427-2.69950.17951450.14532552X-RAY DIFFRACTION99
2.6995-36.8120.18011490.13942697X-RAY DIFFRACTION99

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