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- PDB-9mrd: Crystal Structure of TREX1 Homolog Plex9.1 bound to ssDNA -

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Basic information

Entry
Database: PDB / ID: 9mrd
TitleCrystal Structure of TREX1 Homolog Plex9.1 bound to ssDNA
Components
  • DNA(5'-*AP*CP*TP*GP*A-3')
  • exodeoxyribonuclease III
KeywordsDNA BINDING PROTEIN / DNA Bound / Exonuclease / DEDDh / Innate Immunity
Function / homology
Function and homology information


exodeoxyribonuclease III / 3'-5'-DNA exonuclease activity / DNA catabolic process / nucleic acid binding / metal ion binding / cytoplasm
Similarity search - Function
Three-prime repair exonuclease 1/2 / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
DNA / exodeoxyribonuclease III
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
DNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRogers, C.M. / Langelaan, D.N.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2024-06440 Canada
CitationJournal: To Be Published
Title: Insights into Innate Immunity Through Evolutionarily Conserved DEDDh Exonucleases
Authors: Rogers, C.M. / Langelaan, D.N. / Dellaire, G.
History
DepositionJan 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: exodeoxyribonuclease III
D: DNA(5'-*AP*CP*TP*GP*A-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1885
Polymers23,9562
Non-polymers2323
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-46 kcal/mol
Surface area9580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.000, 96.660, 65.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-442-

HOH

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Components

#1: Protein exodeoxyribonuclease III


Mass: 22755.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: plex9.1, si:ch1073-385f13.3 / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: E7FAN2, exodeoxyribonuclease III
#2: DNA chain DNA(5'-*AP*CP*TP*GP*A-3')


Mass: 1199.844 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 298 K / Method: microbatch / Details: 1.2M trisodium citrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.1808 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1808 Å / Relative weight: 1
ReflectionResolution: 1.55→42 Å / Num. obs: 21395 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 21.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Net I/σ(I): 9.6
Reflection shellResolution: 1.55→1.59 Å / Num. unique obs: 3833 / CC1/2: 0.017

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIXphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→42 Å / SU ML: 0.2147 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.9108
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2206 1070 5 %
Rwork0.1658 20320 -
obs0.1684 21390 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1515 70 11 232 1828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01121658
X-RAY DIFFRACTIONf_angle_d1.0932269
X-RAY DIFFRACTIONf_chiral_restr0.0636258
X-RAY DIFFRACTIONf_plane_restr0.0112281
X-RAY DIFFRACTIONf_dihedral_angle_d10.4654249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.990.31731320.22422507X-RAY DIFFRACTION99.92
1.99-2.090.22571310.16372497X-RAY DIFFRACTION99.96
2.09-2.220.20391320.16242510X-RAY DIFFRACTION100
2.22-2.390.2461330.15862512X-RAY DIFFRACTION99.89
2.39-2.630.2171320.16022520X-RAY DIFFRACTION100
2.63-3.020.23671340.17882537X-RAY DIFFRACTION99.93
3.02-3.80.20531350.15512571X-RAY DIFFRACTION100
3.8-420.20411410.16272666X-RAY DIFFRACTION99.89

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