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- PDB-6a4e: Two linked uridine bound Oligoribonuclease (ORN) from Colwellia p... -

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Basic information

Entry
Database: PDB / ID: 6a4e
TitleTwo linked uridine bound Oligoribonuclease (ORN) from Colwellia psychrerythraea strain 34H
Components
  • Oligoribonuclease
  • RNA (5'-R(P*UP*UP*UP*UP*U)-3')
KeywordsHYDROLASE / Oligoribonuclease / Exonuclease / Colwellia psychrerythraea strain 34H
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / DNA metabolic process / 3'-5'-RNA exonuclease activity / nucleic acid binding / cytoplasm
Similarity search - Function
Oligoribonuclease / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / Oligoribonuclease
Similarity search - Component
Biological speciesColwellia psychrerythraea (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.45 Å
AuthorsLee, C.W. / Park, S. / Lee, J.H.
CitationJournal: Sci Rep / Year: 2019
Title: Structural basis of small RNA hydrolysis by oligoribonuclease (CpsORN) from Colwellia psychrerythraea strain 34H.
Authors: Lee, C.W. / Park, S.H. / Jeong, C.S. / Cha, S.S. / Park, H. / Lee, J.H.
History
DepositionJun 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: 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

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Assembly

Deposited unit
A: Oligoribonuclease
C: Oligoribonuclease
B: RNA (5'-R(P*UP*UP*UP*UP*U)-3')
D: RNA (5'-R(P*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)44,1294
Polymers44,1294
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-35 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.667, 59.667, 236.201
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Oligoribonuclease


Mass: 20578.461 Da / Num. of mol.: 2 / Mutation: D163A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea (strain 34H / ATCC BAA-681) (bacteria)
Strain: 34H / ATCC BAA-681 / Gene: orn, CPS_4379 / Production host: Escherichia coli (E. coli)
References: UniProt: Q47VZ4, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (5'-R(P*UP*UP*UP*UP*U)-3')


Mass: 1485.872 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.75 Å3/Da / Density % sol: 55.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 0.04 M citric acid, 0.06 M Bis-Tris propane pH 6.4, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 18200 / % possible obs: 96.2 % / Redundancy: 21.8 % / Net I/σ(I): 76.1
Reflection shellResolution: 2.45→2.49 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MxDCdata collection
HKL-2000data scaling
RefinementResolution: 2.45→47.34 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.45
RfactorNum. reflection% reflection
Rfree0.2758 927 5.12 %
Rwork0.2367 --
obs0.239 18109 95.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.45→47.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2888 80 0 62 3030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083034
X-RAY DIFFRACTIONf_angle_d1.2044120
X-RAY DIFFRACTIONf_dihedral_angle_d16.6011136
X-RAY DIFFRACTIONf_chiral_restr0.052468
X-RAY DIFFRACTIONf_plane_restr0.006518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4499-2.5790.3461150.27362536X-RAY DIFFRACTION100
2.579-2.74060.3041040.28412505X-RAY DIFFRACTION100
2.7406-2.95220.34781190.27392515X-RAY DIFFRACTION100
2.9522-3.24920.32351510.24382499X-RAY DIFFRACTION100
3.2492-3.71920.2651360.23272546X-RAY DIFFRACTION99
3.7192-4.68520.25371490.20862340X-RAY DIFFRACTION92
4.6852-47.34890.25841530.23462241X-RAY DIFFRACTION83

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