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- PDB-7k33: Crystal structure of Endonuclease Q complex with 27-mer duplex su... -

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Basic information

Entry
Database: PDB / ID: 7k33
TitleCrystal structure of Endonuclease Q complex with 27-mer duplex substrate with an abasic lesion at the active site
Components
  • (DNA (27-MER)) x 2
  • Endonuclease Q
KeywordsHYDROLASE/DNA / HYDROLASE / deamination / HYDROLASE-DNA complex
Function / homologyConserved hypothetical protein CHP00375 / Polymerase/histidinol phosphatase-like / Rubredoxin, iron-binding site / Rubredoxin signature. / metal ion binding / DNA / DNA (> 10) / Phosphotransferase
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 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)61,6046
Polymers61,4483
Non-polymers1553
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-70 kcal/mol
Surface area23960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.500, 151.500, 119.380
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

#1: Protein Endonuclease Q


Mass: 44985.910 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
#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: 8196.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
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: 4.33 Å3/Da / Density % sol: 71.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
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: 3.1→88.3 Å / Num. obs: 17780 / % possible obs: 96 % / Redundancy: 2.5 % / Biso Wilson estimate: 134.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.059 / Rrim(I) all: 0.098 / Net I/σ(I): 7.4 / Num. measured all: 45115
Reflection shell

Diffraction-ID: 1 / Redundancy: 2.6 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.1-3.311.301850533140.7050.9891.641.198
8.77-88.30.02819987730.9990.020.0342794.5

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZB8

5zb8


Resolution: 3.11→88.3 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 35.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 618 5.01 %
Rwork0.1907 11718 -
obs0.1928 12336 67.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 271.32 Å2 / Biso mean: 145.4242 Å2 / Biso min: 49.33 Å2
Refinement stepCycle: final / Resolution: 3.11→88.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3126 1091 3 0 4220
Biso mean--129.77 --
Num. residues----449
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.11-3.430.481340.42155358713
3.43-3.920.34151460.27642888303467
3.92-4.940.24642290.2454133436295
4.94-88.30.19852090.14914144435395
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.39470.5831.89855.9279-0.39637.9836-0.0513-0.1096-0.26990.44570.0140.37781.1769-1.05180.00480.7071-0.06630.14720.8552-0.02090.561420.239728.8827-23.0123
23.81820.31850.60742.8547-1.09537.0875-0.30130.4434-0.0704-0.261-0.1516-0.53540.21280.74890.29280.58450.070.05030.73830.16480.546937.34634.9038-26.5272
35.2226-0.7361-0.41374.48191.12637.9640.0883-0.3626-0.38540.7313-0.1799-0.33131.05181.17410.07511.1570.3674-0.05060.81120.09470.697143.701523.3398-3.2152
47.14360.80891.31215.7771-3.80657.3827-0.40390.1963-1.3925-2.06470.2065-1.09162.5287-0.42630.36542.91210.26870.09771.63850.04091.843838.1335-2.6984-7.2264
56.7079-0.3894.15476.0953-2.95257.8660.18011.3542-1.1958-2.16190.42220.2262.12711.2907-0.3782.9906-0.01930.26012.4278-0.22111.810532.28598.2428-30.9288
61.5987-1.1255-3.04281.11492.68987.69080.23960.25950.2829-0.3832-0.336-0.40430.43081.1720.3432.7820.28550.50772.8629-0.31612.058740.554116.1531-53.169
79.0085-4.1471-1.47464.39214.09754.80831.13850.10431.78010.3913-0.25971.5350.91380.6992-0.73742.72460.52850.46032.8184-0.53341.967642.287115.6104-56.3246
82.68272.3276-3.1542.4893-3.85336.37070.72210.26240.0113-2.8273-2.7-1.20060.1273-1.10510.58382.23910.28350.25431.649-0.31391.190536.751518.6724-30.7759
94.1946-3.1314.41258.4705-5.22586.69670.9544-0.1007-1.0667-1.3412-0.21870.25473.49640.7418-0.72872.78560.26310.13691.520.02761.957137.1723-0.0357-10.5904
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 105 )A1 - 105
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 297 )A106 - 297
3X-RAY DIFFRACTION3chain 'A' and (resid 298 through 395 )A298 - 395
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 10 )B1 - 10
5X-RAY DIFFRACTION5chain 'B' and (resid 11 through 15 )B11 - 15
6X-RAY DIFFRACTION6chain 'B' and (resid 16 through 27 )B16 - 27
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 10 )C1 - 10
8X-RAY DIFFRACTION8chain 'C' and (resid 11 through 15 )C11 - 15
9X-RAY DIFFRACTION9chain 'C' and (resid 16 through 27 )C16 - 27

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