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- PDB-7kiu: Structure of recombinant human DNase1L3 in complex with Mg2+ -

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Basic information

Entry
Database: PDB / ID: 7kiu
TitleStructure of recombinant human DNase1L3 in complex with Mg2+
ComponentsDeoxyribonuclease gamma
KeywordsHYDROLASE / Nuclease / DNA hydrolase / Apoptosis / Lupus / Systemic Lupus Erythematosus / SLE / DNA clearance / Metal ion Nuclease / NET clearance
Function / homology
Function and homology information


regulation of neutrophil mediated cytotoxicity / regulation of acute inflammatory response / DNA nuclease activity / programmed cell death involved in cell development / apoptotic DNA fragmentation / deoxyribonuclease I activity / neutrophil activation involved in immune response / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / calcium ion binding ...regulation of neutrophil mediated cytotoxicity / regulation of acute inflammatory response / DNA nuclease activity / programmed cell death involved in cell development / apoptotic DNA fragmentation / deoxyribonuclease I activity / neutrophil activation involved in immune response / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / calcium ion binding / endoplasmic reticulum / DNA binding / extracellular region / nucleus
Similarity search - Function
Deoxyribonuclease I / Deoxyribonuclease I, active site / Deoxyribonuclease I, conservied site / Deoxyribonuclease I signature 2. / Deoxyribonuclease I signature 1. / deoxyribonuclease I / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily
Similarity search - Domain/homology
Deoxyribonuclease gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsMcCord, J.J. / Keyel, P.A. / Sutton, R.B.
CitationJournal: Commun Biol / Year: 2022
Title: Structural features of Dnase1L3 responsible for serum antigen clearance.
Authors: McCord, J.J. / Engavale, M. / Masoumzadeh, E. / Villarreal, J. / Mapp, B. / Latham, M.P. / Keyel, P.A. / Sutton, R.B.
History
DepositionOct 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxyribonuclease gamma
B: Deoxyribonuclease gamma
C: Deoxyribonuclease gamma
D: Deoxyribonuclease gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,38116
Polymers131,0904
Non-polymers29212
Water3,135174
1
A: Deoxyribonuclease gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8454
Polymers32,7721
Non-polymers733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Deoxyribonuclease gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8454
Polymers32,7721
Non-polymers733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Deoxyribonuclease gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8454
Polymers32,7721
Non-polymers733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Deoxyribonuclease gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8454
Polymers32,7721
Non-polymers733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.313, 72.671, 73.169
Angle α, β, γ (deg.)85.394, 80.558, 88.392
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Deoxyribonuclease gamma / DNase gamma / DNase I homolog protein DHP2 / Liver and spleen DNase / LSD / Deoxyribonuclease I- ...DNase gamma / DNase I homolog protein DHP2 / Liver and spleen DNase / LSD / Deoxyribonuclease I-like 3 / DNase I-like 3 / DNase1L3


Mass: 32772.387 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNASE1L3, DHP2, DNAS1L3 / Plasmid: p202
Details (production host): TEV cleavable MBP-His tagged fusion protein
Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-Gami 2(DE3)
References: UniProt: Q13609, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 19% PEG 8000, 250 mM Magnesium Chloride, 100 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.12709 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Dec 15, 2019
RadiationMonochromator: 1.12709 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 2.21→32.07 Å / Num. obs: 50424 / % possible obs: 94.9 % / Redundancy: 9.1 % / Biso Wilson estimate: 44.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.145 / Rrim(I) all: 0.153 / Net I/σ(I): 8.5
Reflection shellResolution: 2.21→2.25 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.391 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2368 / CC1/2: 0.491 / Rrim(I) all: 1.609 / % possible all: 90.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Blu-Icedata collection
XDSdata scaling
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DNK

1dnk


Resolution: 2.22→32.06 Å / SU ML: 0.4141 / Cross valid method: FREE R-VALUE / Phase error: 30.7442
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2304 2221 4.51 %1
Rwork0.1906 47000 --
obs0.1925 49117 93.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.95 Å2
Refinement stepCycle: LAST / Resolution: 2.22→32.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8700 0 12 174 8886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01528933
X-RAY DIFFRACTIONf_angle_d1.738512070
X-RAY DIFFRACTIONf_chiral_restr0.12271308
X-RAY DIFFRACTIONf_plane_restr0.0091545
X-RAY DIFFRACTIONf_dihedral_angle_d18.00883376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.260.49381180.48052556X-RAY DIFFRACTION81.62
2.26-2.320.51721210.49252361X-RAY DIFFRACTION76
2.32-2.370.37281380.33912766X-RAY DIFFRACTION87.1
2.37-2.440.3541310.31542632X-RAY DIFFRACTION84.52
2.44-2.510.32711330.28922858X-RAY DIFFRACTION90.75
2.51-2.590.30591510.26813078X-RAY DIFFRACTION97.38
2.59-2.680.3081370.24733058X-RAY DIFFRACTION97.56
2.68-2.790.2541400.24273040X-RAY DIFFRACTION97.64
2.79-2.920.32111390.22793086X-RAY DIFFRACTION97.34
2.92-3.070.25851480.2083069X-RAY DIFFRACTION97.72
3.07-3.260.25671480.1883062X-RAY DIFFRACTION97.93
3.27-3.520.21931450.17613061X-RAY DIFFRACTION98.19
3.52-3.870.17921440.16143086X-RAY DIFFRACTION98.21
3.87-4.430.19771390.14783102X-RAY DIFFRACTION98.6
4.43-5.570.17951490.14253095X-RAY DIFFRACTION98.18
5.58-32.060.19411400.16813090X-RAY DIFFRACTION98.45

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