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- PDB-5xgu: Escherichia coli. RNase R -

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Basic information

Entry
Database: PDB / ID: 5xgu
TitleEscherichia coli. RNase R
ComponentsRibonuclease R
KeywordsHYDROLASE / exoribonuclease
Function / homology
Function and homology information


exoribonuclease II / exoribonuclease II activity / RNA binding / cytoplasm
Similarity search - Function
Ribonuclease R winged-helix domain / Ribonuclease R winged-helix domain / RNase II/RNase R, cold shock domain / Ribonuclease B, N-terminal OB domain / Ribonuclease B OB domain / Cold shock domain / Ribonuclease R / Ribonuclease II/ribonuclease R / Ribonuclease II/R, conserved site / Ribonuclease II family signature. ...Ribonuclease R winged-helix domain / Ribonuclease R winged-helix domain / RNase II/RNase R, cold shock domain / Ribonuclease B, N-terminal OB domain / Ribonuclease B OB domain / Cold shock domain / Ribonuclease R / Ribonuclease II/ribonuclease R / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / Ribonuclease II/R / RNB domain / RNB / Cold shock domain / Cold shock protein domain / RNA-binding domain, S1 / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Biological speciesEscherichia coli DEC6A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.846 Å
AuthorsChu, L.Y. / Hsieh, T.J. / Yuan, H.S.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structural insights into RNA unwinding and degradation by RNase R.
Authors: Chu, L.Y. / Hsieh, T.J. / Golzarroshan, B. / Chen, Y.P. / Agrawal, S. / Yuan, H.S.
History
DepositionApr 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
B: Ribonuclease R
A: Ribonuclease R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,7214
Polymers146,6732
Non-polymers492
Water30,2831681
1
A: Ribonuclease R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3612
Polymers73,3361
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area29750 Å2
MethodPISA
2
B: Ribonuclease R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3612
Polymers73,3361
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-8 kcal/mol
Surface area30350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.691, 120.863, 83.626
Angle α, β, γ (deg.)90.00, 91.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribonuclease R / RNase R


Mass: 73336.336 Da / Num. of mol.: 2 / Fragment: UNP residues 87-725 / Mutation: A45V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli DEC6A (bacteria) / Gene: rnr, ECDEC6A_5034 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: H4USN4, exoribonuclease II
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1681 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 8% v/v Tacimate, pH 6.0, 10 % w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 124382 / % possible obs: 99.14 % / Redundancy: 4.5 % / Rsym value: 0.089 / Net I/σ(I): 11.8
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3.7 / Num. unique obs: 48331 / Rsym value: 0.445 / % possible all: 99.14

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VNU

2vnu


Resolution: 1.846→29.671 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 2005 1.61 %
Rwork0.1872 --
obs0.188 124300 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.846→29.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9959 0 2 1681 11642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610152
X-RAY DIFFRACTIONf_angle_d0.67213710
X-RAY DIFFRACTIONf_dihedral_angle_d13.7416148
X-RAY DIFFRACTIONf_chiral_restr0.0451500
X-RAY DIFFRACTIONf_plane_restr0.0041799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8457-1.89180.26861220.22217857X-RAY DIFFRACTION89
1.8918-1.9430.24511490.22288756X-RAY DIFFRACTION100
1.943-2.00020.25351480.21878757X-RAY DIFFRACTION100
2.0002-2.06470.28211420.21338757X-RAY DIFFRACTION100
2.0647-2.13850.26271450.2038777X-RAY DIFFRACTION100
2.1385-2.22410.22621400.19568797X-RAY DIFFRACTION100
2.2241-2.32520.22881410.18878832X-RAY DIFFRACTION100
2.3252-2.44780.25471440.19068803X-RAY DIFFRACTION100
2.4478-2.60110.22361500.19968757X-RAY DIFFRACTION100
2.6011-2.80180.24761470.19938814X-RAY DIFFRACTION100
2.8018-3.08340.28321420.20058847X-RAY DIFFRACTION100
3.0834-3.5290.23731440.18258810X-RAY DIFFRACTION100
3.529-4.44380.21341460.15338836X-RAY DIFFRACTION100
4.4438-29.67480.20321450.17298895X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -12.4535 Å / Origin y: 44.8802 Å / Origin z: -60.9634 Å
111213212223313233
T0.1264 Å20.0028 Å2-0.0031 Å2-0.1212 Å2-0.0288 Å2--0.1487 Å2
L0.059 °2-0.0051 °2-0.0131 °2-0.1242 °2-0.1782 °2--0.3761 °2
S-0.0007 Å °0.014 Å °-0.0072 Å °-0.0233 Å °0.0326 Å °0.0522 Å °-0.0084 Å °-0.0744 Å °-0.0337 Å °
Refinement TLS groupSelection details: all

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