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- PDB-6a4d: pNP-TMP bound Oligoribonuclease (ORN) from Colwellia psychrerythr... -

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Basic information

Entry
Database: PDB / ID: 6a4d
TitlepNP-TMP bound Oligoribonuclease (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
Chem-9RC / Oligoribonuclease
Similarity search - Component
Biological speciesColwellia psychrerythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.19 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
B: Oligoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4956
Polymers41,7212
Non-polymers1,7734
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-10 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.532, 59.532, 236.269
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-303-

HOH

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Components

#1: Protein Oligoribonuclease


Mass: 20860.738 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: Chemical
ChemComp-9RC / 5'-O-[(S)-hydroxy(4-nitrophenoxy)phosphoryl]thymidine / PNP-TMP


Mass: 443.302 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H18N3O10P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.9 Å3/Da / Density % sol: 57.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.4 M ammonium tartrate dibasic, 0.1 M Tris pH 8.5

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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: Nov 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 25387 / % possible obs: 97.8 % / Redundancy: 9.7 % / Net I/σ(I): 38.5
Reflection shellResolution: 2.19→2.24 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
MxDCdata collection
HKL-2000data scaling
RefinementResolution: 2.19→47.25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.266 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27064 1296 5.1 %RANDOM
Rwork0.20474 ---
obs0.20806 24032 97.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.784 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: 2.19→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2918 0 120 147 3185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.023108
X-RAY DIFFRACTIONr_bond_other_d0.0020.022825
X-RAY DIFFRACTIONr_angle_refined_deg1.9652.0014223
X-RAY DIFFRACTIONr_angle_other_deg1.0633.016575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6185364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.67725.07142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44515535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.4251514
X-RAY DIFFRACTIONr_chiral_restr0.1060.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213374
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02600
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
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_it4.4985.1451462
X-RAY DIFFRACTIONr_mcbond_other4.4995.1441461
X-RAY DIFFRACTIONr_mcangle_it6.447.6971824
X-RAY DIFFRACTIONr_mcangle_other6.4397.6971825
X-RAY DIFFRACTIONr_scbond_it5.0815.6561646
X-RAY DIFFRACTIONr_scbond_other5.085.661647
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.6278.3462400
X-RAY DIFFRACTIONr_long_range_B_refined11.30262.3923670
X-RAY DIFFRACTIONr_long_range_B_other11.31662.3093637
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.192→2.249 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 86 -
Rwork0.26 1699 -
obs--95.35 %

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