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- PDB-7k30: Crystal structure of Endonuclease Q complex with 27-mer duplex su... -

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Basic information

Entry
Database: PDB / ID: 7k30
TitleCrystal structure of Endonuclease Q complex with 27-mer duplex substrate with dU 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: 2.34 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)62,05210
Polymers61,6483
Non-polymers4037
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-63 kcal/mol
Surface area23520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.700, 152.700, 118.170
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: 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

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (27-MER)


Mass: 8356.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (27-MER)


Mass: 8306.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 62 molecules

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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 4.3 Å3/Da / Density % sol: 71.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2 M tri-potassium citrate and 15 % (w/v) polyethylene glycol (PEG) 3,350

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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: Aug 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.32→88.12 Å / Num. obs: 44238 / % possible obs: 99.5 % / Redundancy: 11.5 % / Biso Wilson estimate: 50.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.031 / Rrim(I) all: 0.106 / Net I/σ(I): 11.2 / Num. measured all: 509530
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) all% possible allRrim(I) all
2.32-2.4119.943110.3773.34698.9
8.99-88.1211.10.0467650.9990.01499.20.048

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Processing

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

5zb8


Resolution: 2.34→88.12 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.3 / Phase error: 32.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2284 1411 4.94 %
Rwork0.2055 27180 -
obs0.2067 28591 65.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.02 Å2 / Biso mean: 70.5227 Å2 / Biso min: 13.45 Å2
Refinement stepCycle: final / Resolution: 2.34→88.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3126 1101 19 55 4301
Biso mean--54.21 45.97 -
Num. residues----449
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.34-2.420.450371.121211283
2.42-2.520.6917190.567446848711
2.52-2.630.3391580.3794968102624
2.63-2.770.35031020.34881644174640
2.77-2.940.39211440.3413277342179
2.94-3.170.32311980.29341754373100
3.17-3.490.27082020.236541294331100
3.49-3.990.23572030.198341554358100
3.99-5.030.16852410.149941354376100
5.03-88.120.18222370.152141084345100
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)
10.27140.06480.06050.6989-0.26120.9378-0.1958-0.1955-0.22020.15830.12490.06830.6697-0.11560.07450.5317-0.08750.21850.32350.0829-0.126923.986225.4739-17.4449
20.6059-0.28790.13340.76360.17831.9683-0.0827-0.1936-0.19750.11840.04650.25930.5025-0.58580.11870.2194-0.12490.25080.54140.0507-0.176318.253731.1612-26.6581
31.4412-0.3786-0.58151.85690.07024.3786-0.21970.1951-0.076-0.2132-0.11570.23910.5982-0.2952-0.09370.2361-0.1244-0.07340.3509-0.07310.026723.405732.7848-37.422
41.9723-0.24070.04250.79030.16771.8303-0.40010.39880.01170.0643-0.0508-0.23110.21510.4329-0.22490.0450.1312-0.01470.43660.12260.126436.427636.2483-26.5151
51.18990.1064-0.04241.21830.28311.7693-0.12380.4018-0.1745-0.2812-0.2323-0.44120.32080.3556-0.16450.40490.37690.09390.67310.09840.124540.87732.051-23.1693
62.5416-0.4702-0.41791.32020.56310.9709-0.11940.74370.5762-0.09110.1445-0.6143-0.0510.7184-0.02520.16420.0414-0.08390.72960.20610.517146.636143.0566-24.0468
70.8494-0.33-0.07262.4345-0.96620.9195-0.0182-0.3079-0.52530.07320.17510.2571.01740.0741-0.28630.80090.208-0.04730.29860.18210.252438.075120.0189-4.6239
80.95210.5363-0.32231.80080.21360.22350.1245-0.2876-0.30110.2766-0.0653-0.680.44840.67370.19950.6960.6025-0.0830.71950.15220.305547.448725.2915-2.3745
95.4482-0.30540.51156.9401-4.33392.7283-0.0065-0.1041-0.7388-0.72230.22060.50131.4223-0.1372-0.09742.38290.2425-0.10350.8340.29950.92938.0973-2.5016-7.3361
103.7797-4.0994.17695.2967-4.97294.84670.24471.1386-0.9866-0.01750.33810.59211.51670.9577-0.60611.88310.1481-0.13881.0237-0.03240.915532.93298.5112-31.1572
110.12210.26230.02980.58220.06970.00780.11911.00830.0232-0.85450.1812-0.59540.86930.24150.03691.65150.24060.70682.0316-0.37931.063941.93116.2292-54.1905
120.23450.4239-0.27190.9886-0.87360.97850.07720.931-0.08120.23090.0845-0.16580.3686-0.465-0.45732.14980.25450.77132.0817-0.42471.12942.605815.7916-56.0459
131.9099-0.52360.55070.1388-0.15130.15730.5162-0.2584-0.8663-0.0391-0.09020.09961.67020.5473-0.24141.83470.2676-0.01140.670.12090.672537.22665.8225-16.3578
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 45 )A1 - 45
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 105 )A46 - 105
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 131 )A106 - 131
4X-RAY DIFFRACTION4chain 'A' and (resid 132 through 205 )A132 - 205
5X-RAY DIFFRACTION5chain 'A' and (resid 206 through 278 )A206 - 278
6X-RAY DIFFRACTION6chain 'A' and (resid 279 through 298 )A279 - 298
7X-RAY DIFFRACTION7chain 'A' and (resid 299 through 333 )A299 - 333
8X-RAY DIFFRACTION8chain 'A' and (resid 334 through 395 )A334 - 395
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 10 )B1 - 10
10X-RAY DIFFRACTION10chain 'B' and (resid 11 through 15 )B11 - 15
11X-RAY DIFFRACTION11chain 'B' and (resid 17 through 27 )B17 - 27
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 10 )C1 - 10
13X-RAY DIFFRACTION13chain 'C' and (resid 11 through 27 )C11 - 27

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