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- PDB-9mrc: Crystal Structure of TREX1 Homolog Plex9.1 -

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Basic information

Entry
Database: PDB / ID: 9mrc
TitleCrystal Structure of TREX1 Homolog Plex9.1
Componentsexodeoxyribonuclease III
KeywordsDNA BINDING PROTEIN / Exonuclease / TREX1 homolog / DEDDh motif / Apoprotein
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
exodeoxyribonuclease III
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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


Theoretical massNumber of molelcules
Total (without water)22,6981
Polymers22,6981
Non-polymers00
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.290, 96.930, 65.750
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-372-

HOH

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Components

#1: Protein exodeoxyribonuclease III


Mass: 22697.811 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 BL21 (bacteria) / References: UniProt: E7FAN2, exodeoxyribonuclease III
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
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: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 298 K / Method: microbatch / Details: 2.0M ammonium sulfate, 1.2M tri-sodium citrate pH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95371 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95371 Å / Relative weight: 1
ReflectionResolution: 1.44→48.47 Å / Num. obs: 25307 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.051 / Rrim(I) all: 0.131 / Net I/σ(I): 7.6
Reflection shellResolution: 1.44→1.48 Å / Num. unique obs: 4837 / CC1/2: 0.204 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487phasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.46 Å / SU ML: 0.1655 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.2662
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2099 1265 5 %
Rwork0.1717 24036 -
obs0.1736 25301 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.17 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 0 279 1823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00951595
X-RAY DIFFRACTIONf_angle_d1.03332164
X-RAY DIFFRACTIONf_chiral_restr0.0605242
X-RAY DIFFRACTIONf_plane_restr0.0109284
X-RAY DIFFRACTIONf_dihedral_angle_d5.7499215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.870.24391390.19822642X-RAY DIFFRACTION99.93
1.87-1.960.23161380.18832623X-RAY DIFFRACTION99.6
1.96-2.060.25491390.18072640X-RAY DIFFRACTION99.86
2.06-2.190.22141390.16332639X-RAY DIFFRACTION100
2.19-2.360.20261400.15982658X-RAY DIFFRACTION99.75
2.36-2.60.19521400.1642647X-RAY DIFFRACTION99.96
2.6-2.970.21791410.18332680X-RAY DIFFRACTION100
2.97-3.740.20971420.16792697X-RAY DIFFRACTION99.82
3.74-48.460.19031470.16882810X-RAY DIFFRACTION99.76

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