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- PDB-8edd: Staphylococcus aureus endonuclease IV Y33F mutant -

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Basic information

Entry
Database: PDB / ID: 8edd
TitleStaphylococcus aureus endonuclease IV Y33F mutant
ComponentsProbable endonuclease 4
KeywordsHYDROLASE / endonuclease 4 / 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: 1.5 Å
AuthorsSaper, M.A. / Kirillov, S. / Isupov, M.N. / Wiener, R. / Rouvinski, A.
Funding support Israel, Kazakhstan, 2items
OrganizationGrant numberCountry
Other private Israel
Other governmentAP08856811Kazakhstan
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
DepositionSep 4, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2023Provider: 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)33,6739
Polymers33,2001
Non-polymers4738
Water3,513195
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.477, 41.987, 152.773
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: 33199.539 Da / Num. of mol.: 1 / Mutation: Y33F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: nfo, SAR1634 / Plasmid: pET11A-SaNfo(Y33F) / Details (production host): Amp resistant / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): NEBExpress / References: UniProt: Q6GGE2, deoxyribonuclease IV

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Non-polymers , 5 types, 203 molecules

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


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 / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 1.91 Å3/Da / Density % sol: 35.5 % / Description: needle
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein in 20 mM phosphate. Precipitant: 20-30% polyethylene glycol 3350, 200 mM NaCl, 100 mM BisTris, pH 6.5

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Data collection

DiffractionMean temperature: 150 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 25, 2022 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.47→152.77 Å / Num. obs: 41699 / % possible obs: 100 % / Redundancy: 13.19 % / Biso Wilson estimate: 19.04 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.052 / Rrim(I) all: 0.189 / Net I/σ(I): 7.3
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 13.51 % / Rmerge(I) obs: 3.394 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 2173 / CC1/2: 0.305 / Rpim(I) all: 0.955 / Rrim(I) all: 3.527 / % possible all: 99.86

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALS3.dev.683data reduction
xia23.9.dev0data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8AXY

8axy


Resolution: 1.5→40.49 Å / SU ML: 0.2163 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.2523
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2038 3813 4.88 %
Rwork0.1704 74379 -
obs0.1721 41667 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.64 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 16 195 2543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542399
X-RAY DIFFRACTIONf_angle_d0.75553239
X-RAY DIFFRACTIONf_chiral_restr0.0491356
X-RAY DIFFRACTIONf_plane_restr0.0067428
X-RAY DIFFRACTIONf_dihedral_angle_d5.7534318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.34591270.35872570X-RAY DIFFRACTION92.05
1.52-1.540.4151480.35862661X-RAY DIFFRACTION98.77
1.54-1.560.3171280.35062808X-RAY DIFFRACTION99.29
1.56-1.580.32841250.35882763X-RAY DIFFRACTION99.31
1.58-1.610.4171320.33532744X-RAY DIFFRACTION99.41
1.61-1.630.31221060.30732781X-RAY DIFFRACTION99.11
1.63-1.660.3561410.28552762X-RAY DIFFRACTION99.79
1.66-1.690.33021220.27182828X-RAY DIFFRACTION99.86
1.69-1.720.30931170.26352757X-RAY DIFFRACTION99.9
1.72-1.750.25991560.23442795X-RAY DIFFRACTION99.97
1.75-1.790.24921460.21142730X-RAY DIFFRACTION100
1.79-1.820.20491620.19422728X-RAY DIFFRACTION99.97
1.82-1.870.25971290.18292789X-RAY DIFFRACTION100
1.87-1.910.22451690.1792733X-RAY DIFFRACTION100
1.91-1.970.20361590.17672765X-RAY DIFFRACTION99.97
1.97-2.020.23151460.16562726X-RAY DIFFRACTION100
2.02-2.090.22861110.15492821X-RAY DIFFRACTION100
2.09-2.160.21881520.13812717X-RAY DIFFRACTION100
2.16-2.250.21961510.14552776X-RAY DIFFRACTION100
2.25-2.350.16421540.13362773X-RAY DIFFRACTION99.97
2.35-2.480.18181320.14662826X-RAY DIFFRACTION100
2.48-2.630.16191550.14762763X-RAY DIFFRACTION100
2.63-2.830.20532060.14492652X-RAY DIFFRACTION100
2.83-3.120.17421550.15162733X-RAY DIFFRACTION100
3.12-3.570.19051150.14272847X-RAY DIFFRACTION100
3.57-4.50.14271260.13122757X-RAY DIFFRACTION100
4.5-40.490.16411430.15572774X-RAY DIFFRACTION100

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