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- PDB-5zo3: apo form of the nuclease -

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Basic information

Entry
Database: PDB / ID: 5zo3
Titleapo form of the nuclease
ComponentsPutative 3'-5' exonuclease family protein
KeywordsHYDROLASE / nuclease
Function / homology3'-5' exonuclease / 3'-5' exonuclease / 3'-5' exonuclease domain / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / Ribonuclease H superfamily / nucleic acid binding / Ribonuclease H-like superfamily / Putative 3'-5' exonuclease family protein
Function and homology information
Biological speciesAgrobacterium fabrum str. J-07 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.493 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 / 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: Putative 3'-5' exonuclease family protein
B: Putative 3'-5' exonuclease family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3087
Polymers46,8952
Non-polymers4125
Water12,196677
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)189,23128
Polymers187,5818
Non-polymers1,64920
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 area22460 Å2
ΔGint-153 kcal/mol
Surface area62940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.257, 121.257, 133.898
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-458-

HOH

21B-509-

HOH

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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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 677 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
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 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.49→34.47 Å / Num. obs: 80479 / % possible obs: 99.3 % / Redundancy: 14.4 % / Net I/σ(I): 50.45
Reflection shellResolution: 1.49→1.54 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_3092: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.493→34.461 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.4
RfactorNum. reflection% reflection
Rfree0.1742 2000 2.49 %
Rwork0.1558 --
obs0.1562 80477 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.493→34.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3233 0 23 677 3933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063353
X-RAY DIFFRACTIONf_angle_d0.8294549
X-RAY DIFFRACTIONf_dihedral_angle_d2.8031952
X-RAY DIFFRACTIONf_chiral_restr0.078516
X-RAY DIFFRACTIONf_plane_restr0.006590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4932-1.53050.1971400.16155521X-RAY DIFFRACTION100
1.5305-1.57190.17511410.15315532X-RAY DIFFRACTION100
1.5719-1.61820.21071420.1495536X-RAY DIFFRACTION100
1.6182-1.67040.14681410.1495546X-RAY DIFFRACTION100
1.6704-1.73010.1861420.1515568X-RAY DIFFRACTION100
1.7301-1.79940.17421410.15315543X-RAY DIFFRACTION100
1.7994-1.88130.21021430.15865585X-RAY DIFFRACTION100
1.8813-1.98040.19471420.15155567X-RAY DIFFRACTION100
1.9804-2.10450.15511420.14725595X-RAY DIFFRACTION100
2.1045-2.2670.17761430.14845599X-RAY DIFFRACTION100
2.267-2.4950.15611430.16365616X-RAY DIFFRACTION100
2.495-2.85590.18831450.16345670X-RAY DIFFRACTION100
2.8559-3.59760.15791450.15915689X-RAY DIFFRACTION100
3.5976-34.47040.17081500.15655910X-RAY DIFFRACTION100

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