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- PDB-8pkb: Staphylococcus aureus endonuclease IV with bound phosphate -

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Basic information

Entry
Database: PDB / ID: 8pkb
TitleStaphylococcus aureus endonuclease IV with bound phosphate
ComponentsProbable endonuclease 4
KeywordsHYDROLASE / endonuclease IV / DNA repair / metalloenzyme / mutant
Function / homology
Function and homology information


deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / DNA repair / DNA binding / zinc ion binding
Similarity search - Function
AP endonucleases family 2 signature 1. / AP endonucleases family 2 signature 2. / AP endonuclease 2, zinc binding site / AP endonucleases family 2 signature 3. / AP endonucleases family 2 profile. / AP endonuclease 2 / AP endonuclease family 2 / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
: / PHOSPHATE ION / Probable endonuclease 4
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSaper, M. / Kirillov, S. / Rouvinski, A.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Octahedrally coordinated iron in the catalytic site of endonuclease IV from Staphylococcus aureus
Authors: Kirillov, S. / Isupov, M.N. / Paterson, N. / Wiener, R. / Abeldenov, S. / Saper, M.A. / Rouvinski, A.
History
DepositionJun 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable endonuclease 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5597
Polymers33,2161
Non-polymers3436
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.548, 84.040, 103.344
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, 1 molecules A

#1: Protein Probable endonuclease 4 / Endodeoxyribonuclease IV / Endonuclease IV


Mass: 33215.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: nfo, SAR1634 / Plasmid: pET11b-SaNfo / Details (production host): Amp resistant / Production host: Escherichia coli (E. coli) / Strain (production host): BH110(DE3) / References: UniProt: Q6GGE2, deoxyribonuclease IV

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Non-polymers , 5 types, 180 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.51 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200 nl protein mixed with 200 nl precipitant Protein: 9 mg/ml in 20 mM Tris-HCl pH 8.0, 150 mM NaCl was mixed with 20 mM phosphate (final concentration). Precipitant: 28% PEG 3350, 250 mM ...Details: 200 nl protein mixed with 200 nl precipitant Protein: 9 mg/ml in 20 mM Tris-HCl pH 8.0, 150 mM NaCl was mixed with 20 mM phosphate (final concentration). Precipitant: 28% PEG 3350, 250 mM NaCl, 100 mM Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2023
RadiationMonochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.9→44 Å / Num. obs: 50721 / % possible obs: 99.82 % / Redundancy: 5.9 % / Biso Wilson estimate: 30.48 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.2088 / Rpim(I) all: 0.09284 / Rrim(I) all: 0.229 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obs% possible allRrim(I) all
3.79-445.490.09220362499.97
3.01-3.795.930.1953458100
2.63-3.016.170.3239.234151000.352
2.39-2.635.820.4315.8339199.940.472
2.22-2.395.740.5824.233901000.638
2.09-2.225.930.6623.133871000.724
1.98-2.096.080.9542.01335199.971.045
1.9-1.986.141.1651.533431002.278

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44 Å / SU ML: 0.2396 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 22.3196
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2112 2586 5.1 %
Rwork0.1877 48135 -
obs0.1888 50721 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.89 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 10 174 2517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642425
X-RAY DIFFRACTIONf_angle_d0.75953279
X-RAY DIFFRACTIONf_chiral_restr0.0496359
X-RAY DIFFRACTIONf_plane_restr0.0069435
X-RAY DIFFRACTIONf_dihedral_angle_d5.4943327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.33311520.30532715X-RAY DIFFRACTION99.55
1.94-1.980.34121770.28632599X-RAY DIFFRACTION99.71
1.98-2.020.28791580.27842704X-RAY DIFFRACTION99.76
2.02-2.070.27281540.26752633X-RAY DIFFRACTION99.68
2.07-2.120.27681470.24482711X-RAY DIFFRACTION99.44
2.12-2.170.30061540.2352651X-RAY DIFFRACTION99.57
2.17-2.240.24561530.23242693X-RAY DIFFRACTION99.16
2.24-2.310.26581340.232670X-RAY DIFFRACTION99.12
2.31-2.390.27771370.22142704X-RAY DIFFRACTION99.72
2.39-2.490.26751390.20232661X-RAY DIFFRACTION99.47
2.49-2.60.21131540.20222685X-RAY DIFFRACTION99.61
2.6-2.740.20641270.18972711X-RAY DIFFRACTION99.86
2.74-2.910.24431340.18442686X-RAY DIFFRACTION99.37
2.91-3.140.23551280.18452709X-RAY DIFFRACTION99.3
3.14-3.450.18531510.16192643X-RAY DIFFRACTION98.59
3.45-3.950.19221050.15672664X-RAY DIFFRACTION97.91
3.95-4.980.13021450.13262625X-RAY DIFFRACTION97.43
4.98-440.17611370.18262671X-RAY DIFFRACTION98.8

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