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- PDB-9l55: Plastid Localized Exonuclease 1 (D249A) complexed with DNA -

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Basic information

Entry
Database: PDB / ID: 9l55
TitlePlastid Localized Exonuclease 1 (D249A) complexed with DNA
Components
  • 5'-3' exonuclease family protein
  • DNA (5'-D(P*AP*TP*TP*AP*AP*GP*TP*GP*GP*T)-3')
  • DNA (5'-D(P*GP*TP*GP*AP*GP*GP*TP*A)-3')
  • DNA (5'-D(P*TP*AP*CP*CP*TP*CP*AP*CP*AP*CP*CP*AP*CP*TP*TP*AP*AP*T)-3')
KeywordsPLANT PROTEIN/DNA / Exonuclease / PLANT PROTEIN-DNA complex
Function / homology
Function and homology information


DNA replication, Okazaki fragment processing / 5'-flap endonuclease activity / 5'-3' exonuclease activity / DNA-directed DNA polymerase activity / DNA binding
Similarity search - Function
Flap endonuclease / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / 5'-3' exonuclease family protein
Similarity search - Component
Biological speciesZea mays (maize)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsShi, G. / Zhang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32425006 China
CitationJournal: Nat.Plants / Year: 2025
Title: PEN1 catalyses RNA primer removal during plastid DNA replication in maize.
Authors: Huang, X. / Shi, G. / Xiao, Q. / Feng, J. / Huang, Y. / Shi, H. / Wang, Q. / Su, Y. / Wang, J. / Wu, X. / Cao, Y. / Wang, H. / Wang, W. / Zhang, Y. / Wu, Y.
History
DepositionDec 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-3' exonuclease family protein
B: 5'-3' exonuclease family protein
E: DNA (5'-D(P*TP*AP*CP*CP*TP*CP*AP*CP*AP*CP*CP*AP*CP*TP*TP*AP*AP*T)-3')
F: DNA (5'-D(P*AP*TP*TP*AP*AP*GP*TP*GP*GP*T)-3')
G: DNA (5'-D(P*GP*TP*GP*AP*GP*GP*TP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4789
Polymers84,3805
Non-polymers974
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.450, 104.400, 117.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 5'-3' exonuclease family protein / Plastid Localized Exonuclease 1 / DNA polymerase I


Mass: 36697.551 Da / Num. of mol.: 2 / Mutation: D249A
Source method: isolated from a genetically manipulated source
Details: Expression using the pET28a-His-SUMOstar plasmid.Deleted the first 91 amino acids of the original sequence and the D249 mutation became A249(the deleted sequence was the signal peptide).
Source: (gene. exp.) Zea mays (maize) / Gene: LOC100285516, ZEAMMB73_Zm00001d047988 / Plasmid: pET28a-His-SUMOstar / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: B4FJZ1

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DNA chain , 3 types, 3 molecules EFG

#2: DNA chain DNA (5'-D(P*TP*AP*CP*CP*TP*CP*AP*CP*AP*CP*CP*AP*CP*TP*TP*AP*AP*T)-3')


Mass: 5379.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*AP*TP*TP*AP*AP*GP*TP*GP*GP*T)-3')


Mass: 3099.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*TP*GP*AP*GP*GP*TP*A)-3')


Mass: 2506.665 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 2 types, 50 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.5 Å3/Da / Density % sol: 64.87 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium acetate, 0.01 M MgCl2, 0.05 M Sodium cacodylate pH 6.5, 10% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2024
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.87→30.38 Å / Num. obs: 51965 / % possible obs: 99.8 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.04 / Rrim(I) all: 0.145 / Net I/σ(I): 19.3
Reflection shellResolution: 2.87→2.94 Å / Redundancy: 13.2 % / Rmerge(I) obs: 1.79 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 26697 / CC1/2: 0.739 / Rpim(I) all: 0.647 / Rsym value: 1.69 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
xia2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.87→30.38 Å / SU ML: 0.4526 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.7262
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3151 3739 7.2 %
Rwork0.2687 48226 -
obs0.272 51965 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.24 Å2
Refinement stepCycle: LAST / Resolution: 2.87→30.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4452 741 4 46 5243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00725371
X-RAY DIFFRACTIONf_angle_d1.10117445
X-RAY DIFFRACTIONf_chiral_restr0.0901871
X-RAY DIFFRACTIONf_plane_restr0.0065826
X-RAY DIFFRACTIONf_dihedral_angle_d20.99091996
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-2.910.36421390.38811788X-RAY DIFFRACTION99.23
2.91-2.940.35751210.37251812X-RAY DIFFRACTION99.69
2.94-2.980.37151510.38321800X-RAY DIFFRACTION98.99
2.98-3.030.34561500.361788X-RAY DIFFRACTION99.49
3.03-3.070.46161230.35181789X-RAY DIFFRACTION99.12
3.07-3.120.37961730.35091703X-RAY DIFFRACTION98.84
3.12-3.170.38721340.34681806X-RAY DIFFRACTION99.18
3.17-3.230.41241180.30941822X-RAY DIFFRACTION99.03
3.23-3.280.34881360.29561759X-RAY DIFFRACTION99.16
3.29-3.350.33971390.28091796X-RAY DIFFRACTION98.83
3.35-3.420.36241300.2861782X-RAY DIFFRACTION98.96
3.42-3.490.36861360.29721780X-RAY DIFFRACTION99.69
3.49-3.570.34671540.30231776X-RAY DIFFRACTION98.87
3.57-3.660.36141330.27531775X-RAY DIFFRACTION99.17
3.66-3.760.37451480.29621769X-RAY DIFFRACTION99.17
3.76-3.870.33761310.28771793X-RAY DIFFRACTION99.48
3.87-3.990.30021370.26691801X-RAY DIFFRACTION99.85
3.99-4.140.31831490.25761766X-RAY DIFFRACTION99.69
4.14-4.30.27871300.2331793X-RAY DIFFRACTION99.38
4.3-4.50.27711420.22381806X-RAY DIFFRACTION99.49
4.5-4.730.27411240.23521809X-RAY DIFFRACTION100
4.73-5.030.35541500.24031779X-RAY DIFFRACTION100
5.03-5.410.28461340.27421804X-RAY DIFFRACTION99.9
5.42-5.960.31421310.29511798X-RAY DIFFRACTION99.84
5.96-6.810.35721430.2831803X-RAY DIFFRACTION99.9
6.81-8.540.29251470.25251786X-RAY DIFFRACTION99.95
8.55-30.380.22131360.21721743X-RAY DIFFRACTION97.06

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