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- PDB-6a4a: Oligoribonuclease (ORN) from Colwellia psychrerythraea strain 34H -

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Basic information

Entry
Database: PDB / ID: 6a4a
TitleOligoribonuclease (ORN) from Colwellia psychrerythraea strain 34H
ComponentsOligoribonuclease
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
Biological speciesColwellia psychrerythraea 34H (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6472
Polymers20,6221
Non-polymers241
Water41423
1
A: Oligoribonuclease
hetero molecules

A: Oligoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2944
Polymers41,2452
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area3230 Å2
ΔGint-16 kcal/mol
Surface area16590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.112, 53.112, 143.338
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Oligoribonuclease


Mass: 20622.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea 34H (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: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 15% (w/v) PEG 3350, 0.1 M magnesium formate

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Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→53.11 Å / Num. obs: 6155 / % possible obs: 99.8 % / Redundancy: 22.7 % / Net I/σ(I): 56.6
Reflection shellResolution: 2.7→2.77 Å

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
MxDCdata collection
HKL-2000data scaling
HKL-2000data reduction
RefinementResolution: 2.7→35.521 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 40.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2974 303 4.98 %RANDOM
Rwork0.2549 ---
obs0.2575 6088 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→35.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 1 23 1463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011469
X-RAY DIFFRACTIONf_angle_d1.1291990
X-RAY DIFFRACTIONf_dihedral_angle_d11.631887
X-RAY DIFFRACTIONf_chiral_restr0.059223
X-RAY DIFFRACTIONf_plane_restr0.006257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-3.40150.39421310.2992818X-RAY DIFFRACTION99
3.4015-35.52430.2791720.24442967X-RAY DIFFRACTION99

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