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- PDB-6h0r: X-ray structure of SRS2 fragment of Rgs4 3' UTR -

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Basic information

Entry
Database: PDB / ID: 6h0r
TitleX-ray structure of SRS2 fragment of Rgs4 3' UTR
ComponentsSRS2 fragment of Rgs4 3' UTR, RNA (31-MER)
KeywordsRNA / Rgs4
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.73 Å
AuthorsHeber, S. / Janowski, R. / Niessing, D.
CitationJournal: Nat Commun / Year: 2019
Title: Staufen2-mediated RNA recognition and localization requires combinatorial action of multiple domains.
Authors: Heber, S. / Gaspar, I. / Tants, J.N. / Gunther, J. / Moya, S.M.F. / Janowski, R. / Ephrussi, A. / Sattler, M. / Niessing, D.
History
DepositionJul 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 15, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SRS2 fragment of Rgs4 3' UTR, RNA (31-MER)
B: SRS2 fragment of Rgs4 3' UTR, RNA (31-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,47215
Polymers19,8002
Non-polymers1,67213
Water2,090116
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A: SRS2 fragment of Rgs4 3' UTR, RNA (31-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7488
Polymers9,9001
Non-polymers8487
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-63 kcal/mol
Surface area5420 Å2
MethodPISA
2
B: SRS2 fragment of Rgs4 3' UTR, RNA (31-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7247
Polymers9,9001
Non-polymers8246
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-61 kcal/mol
Surface area5770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.020, 32.390, 46.370
Angle α, β, γ (deg.)90.00, 103.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: RNA chain SRS2 fragment of Rgs4 3' UTR, RNA (31-MER)


Mass: 9899.846 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat)
#2: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ba
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.1 Å3/Da / Density % sol: 41.51 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: sodium cacodylate, NaCl, BaCl2, MPD, spermine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 8, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→39.818 Å / Num. obs: 16965 / % possible obs: 96.7 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Net I/σ(I): 17.9
Reflection shellResolution: 1.73→1.775 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 1218 / CC1/2: 0.757 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MAD / Resolution: 1.73→39.818 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.33
RfactorNum. reflection% reflection
Rfree0.2373 820 4.83 %
Rwork0.1847 --
obs0.1872 16965 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.73→39.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1290 13 116 1419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041439
X-RAY DIFFRACTIONf_angle_d0.912237
X-RAY DIFFRACTIONf_dihedral_angle_d11.58734
X-RAY DIFFRACTIONf_chiral_restr0.037306
X-RAY DIFFRACTIONf_plane_restr0.00760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.83840.27711200.24612629X-RAY DIFFRACTION95
1.8384-1.98030.2761320.22642641X-RAY DIFFRACTION96
1.9803-2.17960.28061310.20722668X-RAY DIFFRACTION97
2.1796-2.4950.2611370.20422703X-RAY DIFFRACTION97
2.495-3.14320.25281420.21472710X-RAY DIFFRACTION98
3.1432-100.21091580.15382794X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -14.5114 Å / Origin y: 15.0598 Å / Origin z: 28.3249 Å
111213212223313233
T0.2793 Å20.0081 Å20.0087 Å2-0.3226 Å2-0.0111 Å2--0.2887 Å2
L0.288 °20.0368 °20.1446 °2-0.103 °20.0645 °2--0.3386 °2
S0.0146 Å °-0.042 Å °0.0543 Å °0.0808 Å °-0.0014 Å °0.0525 Å °0.0849 Å °0.1738 Å °-0.0395 Å °
Refinement TLS groupSelection details: all

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