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- PDB-7k31: Crystal structure of Endonuclease Q complex with 27-mer duplex su... -

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Basic information

Entry
Database: PDB / ID: 7k31
TitleCrystal structure of Endonuclease Q complex with 27-mer duplex substrate with dI at the active site
Components
  • (DNA (27-MER)) x 2
  • Endonuclease Q
KeywordsHYDROLASE/DNA / HYDROLASE / deamination / HYDROLASE-DNA complex
Function / homology
Function and homology information


Conserved hypothetical protein CHP00375 / Polymerase/histidinol phosphatase-like / Rubredoxin, iron-binding site / Rubredoxin signature. / Metal-dependent hydrolases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Phosphotransferase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsShi, K. / Moeller, N.M. / Banerjee, S. / Yin, L. / Orellana, K. / Aihara, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structural basis for recognition of distinct deaminated DNA lesions by endonuclease Q.
Authors: Shi, K. / Moeller, N.H. / Banerjee, S. / McCann, J.L. / Carpenter, M.A. / Yin, L. / Moorthy, R. / Orellana, K. / Harki, D.A. / Harris, R.S. / Aihara, H.
History
DepositionSep 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endonuclease Q
B: DNA (27-MER)
C: DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,40710
Polymers61,0533
Non-polymers3547
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-126 kcal/mol
Surface area23340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.120, 151.120, 117.580
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Endonuclease Q


Mass: 44456.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: I6V2I0

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (27-MER)


Mass: 8266.292 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (27-MER)


Mass: 8330.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 15 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 4.2 Å3/Da / Density % sol: 70.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 15 mM Tris-HCl pH 7.4, 0.15 M NaCl, 1 mM MgCl2, and 4 mM beta-mercaptoethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.85→87.47 Å / Num. obs: 22027 / % possible obs: 94.2 % / Redundancy: 2.3 % / Biso Wilson estimate: 42.82 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.045 / Rrim(I) all: 0.072 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.85-32.41.01783032970.7960.821.3051.296.2
9.01-87.462.30.0315186550.9860.0260.043490

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZB8

5zb8


Resolution: 2.88→87.47 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 24.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2383 790 5.18 %
Rwork0.1821 14475 -
obs0.185 15265 67.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.65 Å2 / Biso mean: 58.4722 Å2 / Biso min: 4.9 Å2
Refinement stepCycle: final / Resolution: 2.88→87.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3126 1101 10 8 4245
Biso mean--37.21 15.53 -
Num. residues----449
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.88-3.060.3858130.34853163299
3.06-3.30.3104730.25121146121932
3.3-3.630.33251510.23312954310583
3.63-4.160.24031980.19513434363296
4.16-5.240.19711510.15143322347393
5.24-87.470.20112040.15283303350793
Refinement TLS params.

L11: 0 °2 / L12: 0 °2 / L13: 0 °2 / L22: 0 °2 / L23: 0 °2 / L33: 0 °2 / S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDOrigin x (Å)Origin y (Å)Origin z (Å)
121.200327.6937-20.7602
229.306735.8485-27.7059
347.457227.3858-26.7755
444.712235.5335-18.0304
536.78421.4701-0.3034
650.888223.8122-4.3763
738.1174-2.7842-7.2931
832.51147.8306-30.8639
940.50515.6935-52.5493
1042.276515.1293-55.5164
1137.04975.566-16.3908
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 91 )A1 - 91
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 224 )A92 - 224
3X-RAY DIFFRACTION3chain 'A' and (resid 225 through 278 )A225 - 278
4X-RAY DIFFRACTION4chain 'A' and (resid 279 through 312 )A279 - 312
5X-RAY DIFFRACTION5chain 'A' and (resid 313 through 352 )A313 - 352
6X-RAY DIFFRACTION6chain 'A' and (resid 353 through 395 )A353 - 395
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 10 )B1 - 10
8X-RAY DIFFRACTION8chain 'B' and (resid 11 through 15 )B11 - 15
9X-RAY DIFFRACTION9chain 'B' and (resid 16 through 27 )B16 - 27
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 10 )C1 - 10
11X-RAY DIFFRACTION11chain 'C' and (resid 11 through 27 )C11 - 27

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