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- PDB-6a4f: Separated uridine bound Oligoribonuclease (ORN) from Colwellia ps... -

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Basic information

Database: PDB / ID: 6a4f
TitleSeparated uridine bound Oligoribonuclease (ORN) from Colwellia psychrerythraea strain 34H
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 / 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
: / URIDINE-5'-MONOPHOSPHATE / Oligoribonuclease
Similarity search - Component
Biological speciesColwellia psychrerythraea (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.21 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.
DepositionJun 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release

Structure visualization

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Deposited unit
A: Oligoribonuclease
B: Oligoribonuclease
hetero molecules

Theoretical massNumber of molelcules
Total (without water)43,1908

  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-51 kcal/mol
Surface area15520 Å2
Unit cell
Length a, b, c (Å)59.285, 59.285, 234.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221


#1: Protein Oligoribonuclease / Oligonucleotidase

Mass: 20891.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea (strain 34H / ATCC BAA-681) (unknown)
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-U5P / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate

Mass: 324.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Chemical ChemComp-MN / MANGANESE (II) ION

Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

Experimental details


ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium thiocyanate, 20% (w/v) PEG 3350

Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. obs: 21675 / % possible obs: 86.2 % / Redundancy: 4.8 % / Net I/σ(I): 43.9
Reflection shellResolution: 2.21→2.25 Å


MxDCdata collection
HKL-2000data scaling
RefinementResolution: 2.21→47.02 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.515 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.25 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27018 1031 4.8 %RANDOM
Rwork0.19304 ---
obs0.19674 20644 86.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 57.033 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.21→47.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2930 0 86 181 3197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193080
X-RAY DIFFRACTIONr_bond_other_d0.0020.022806
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.9864182
X-RAY DIFFRACTIONr_angle_other_deg1.05236542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7965364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.91725.139144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.71515542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.7721514
X-RAY DIFFRACTIONr_chiral_restr0.1070.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213330
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02588
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.9335.6151462
X-RAY DIFFRACTIONr_mcbond_other4.935.6131461
X-RAY DIFFRACTIONr_mcangle_it6.7168.4021824
X-RAY DIFFRACTIONr_mcangle_other6.7168.4031825
X-RAY DIFFRACTIONr_scbond_it5.2886.021618
X-RAY DIFFRACTIONr_scbond_other5.2856.0191617
X-RAY DIFFRACTIONr_scangle_other7.3598.8972359
X-RAY DIFFRACTIONr_long_range_B_refined9.41667.4183595
X-RAY DIFFRACTIONr_long_range_B_other9.39767.2013549
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.205→2.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 77 -
Rwork0.276 1473 -
obs--86.06 %

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