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- PDB-5zo5: active state of the nuclease -

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Basic information

Entry
Database: PDB / ID: 5zo5
Titleactive state of the nuclease
ComponentsPutative 3'-5' exonuclease family protein
KeywordsHYDROLASE / nuclease / DEDDy
Function / homology
Function and homology information


3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleic acid binding
Similarity search - Function
3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
: / Putative 3'-5' exonuclease family protein
Similarity search - Component
Biological speciesAgrobacterium fabrum str. J-07 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.297 Å
AuthorsYuan, Z.L. / Gu, L.C.
CitationJournal: Front Microbiol / Year: 2018
Title: NrnC, an RNase D-Like Protein FromAgrobacterium, Is a Novel Octameric Nuclease That Specifically Degrades dsDNA but Leaves dsRNA Intact.
Authors: Yuan, Z. / Gao, F. / Yin, K. / Gu, L.
History
DepositionApr 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative 3'-5' exonuclease family protein
B: Putative 3'-5' exonuclease family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,59511
Polymers46,8952
Non-polymers7009
Water4,612256
1
A: Putative 3'-5' exonuclease family protein
B: Putative 3'-5' exonuclease family protein
hetero molecules

A: Putative 3'-5' exonuclease family protein
B: Putative 3'-5' exonuclease family protein
hetero molecules

A: Putative 3'-5' exonuclease family protein
B: Putative 3'-5' exonuclease family protein
hetero molecules

A: Putative 3'-5' exonuclease family protein
B: Putative 3'-5' exonuclease family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,38244
Polymers187,5818
Non-polymers2,80036
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area24780 Å2
ΔGint-375 kcal/mol
Surface area62680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.743, 121.743, 149.971
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Putative 3'-5' exonuclease family protein / nuclease


Mass: 23447.658 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum str. J-07 (bacteria)
Gene: AGR8A_Lc10769 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1S7QSB2, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.96 Å3/Da / Density % sol: 58.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris-HCl, pH 8.0, 1 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.297→50 Å / Num. obs: 24603 / % possible obs: 96.8 % / Redundancy: 12.2 % / Net I/σ(I): 28.9
Reflection shellResolution: 2.3→2.38 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2992: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.297→47.26 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.72
RfactorNum. reflection% reflection
Rfree0.2245 1997 8.74 %
Rwork0.1857 --
obs0.189 22848 89.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.297→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3223 0 29 256 3508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023312
X-RAY DIFFRACTIONf_angle_d0.4114494
X-RAY DIFFRACTIONf_dihedral_angle_d2.0492350
X-RAY DIFFRACTIONf_chiral_restr0.04510
X-RAY DIFFRACTIONf_plane_restr0.003579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2966-2.3540.3399860.2393897X-RAY DIFFRACTION56
2.354-2.41760.24951030.23461076X-RAY DIFFRACTION66
2.4176-2.48880.27151170.21841218X-RAY DIFFRACTION74
2.4888-2.56910.25881220.2141268X-RAY DIFFRACTION78
2.5691-2.66090.24771360.21081433X-RAY DIFFRACTION87
2.6609-2.76740.251500.20021557X-RAY DIFFRACTION94
2.7674-2.89340.25081550.21341620X-RAY DIFFRACTION99
2.8934-3.04590.23111580.20721652X-RAY DIFFRACTION100
3.0459-3.23670.27181590.20721653X-RAY DIFFRACTION100
3.2367-3.48650.25911590.19541657X-RAY DIFFRACTION100
3.4865-3.83720.17041590.16921662X-RAY DIFFRACTION100
3.8372-4.39210.20231610.15251687X-RAY DIFFRACTION100
4.3921-5.53230.18081630.15151688X-RAY DIFFRACTION100
5.5323-47.26990.21541690.18461783X-RAY DIFFRACTION99

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