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- PDB-8axy: Staphylococcus aureus endonuclease IV orthorhombic crystal form -

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Basic information

Entry
Database: PDB / ID: 8axy
TitleStaphylococcus aureus endonuclease IV orthorhombic crystal form
ComponentsProbable endonuclease 4
KeywordsHYDROLASE / endonuclease 4 / DNA repair / metalloenzyme
Function / homology
Function and homology information


deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / phosphoric diester hydrolase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision 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 family 2 / AP endonuclease 2 / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel ...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 family 2 / AP endonuclease 2 / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / Probable endonuclease 4
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsRouvinski, A. / Kirillov, S. / Saper, M.A. / Wiener, R. / Isupov, M.N.
Funding support Israel, Kazakhstan, 2items
OrganizationGrant numberCountry
Jacob and Lena Joels Memorial Foundation, Hebrew University of Jerusalem Israel
Ministry of Education and Science of the Republic of KazakhstanAP08856811Kazakhstan
CitationJournal: Biochemistry / Year: 2024
Title: Octahedral Iron in Catalytic Sites of Endonuclease IV from Staphylococcus aureus and Escherichia coli.
Authors: Kirillov, S. / Isupov, M. / Paterson, N.G. / Wiener, R. / Abeldenov, S. / Saper, M.A. / Rouvinski, A.
History
DepositionSep 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable endonuclease 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,54516
Polymers33,2161
Non-polymers1,33015
Water9,386521
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-200 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.857, 82.581, 105.091
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6GGE2, deoxyribonuclease IV
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: - 0.1 M HEPES pH 7.0 - 2.2 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.8 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.05→52.545 Å / Num. obs: 156665 / % possible obs: 99.1 % / Redundancy: 7.2 % / CC1/2: 1 / Rmerge(I) obs: 0.063 / Net I/σ(I): 14.2
Reflection shellResolution: 1.05→1.07 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.882 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 7372 / CC1/2: 0.319 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1xp3

1xp3


Resolution: 1.05→52.545 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.164 / SU ML: 0.023 / Cross valid method: FREE R-VALUE / ESU R: 0.024 / ESU R Free: 0.025
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1577 7783 4.975 %
Rwork0.1358 148645 -
all0.137 --
obs-156428 98.942 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.324 Å2
Baniso -1Baniso -2Baniso -3
1--0.042 Å20 Å20 Å2
2--0.795 Å2-0 Å2
3----0.754 Å2
Refinement stepCycle: LAST / Resolution: 1.05→52.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 63 521 2917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132718
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162591
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.6493712
X-RAY DIFFRACTIONr_angle_other_deg1.5051.5936047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.015369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.18424.248153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2115533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4111513
X-RAY DIFFRACTIONr_chiral_restr0.090.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023115
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02591
X-RAY DIFFRACTIONr_nbd_refined0.2110.2563
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1690.22435
X-RAY DIFFRACTIONr_nbtor_refined0.170.21266
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21170
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2376
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1980.218
X-RAY DIFFRACTIONr_nbd_other0.1820.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1530.234
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0230.21
X-RAY DIFFRACTIONr_mcbond_it1.1261.2351263
X-RAY DIFFRACTIONr_mcbond_other1.1241.2331262
X-RAY DIFFRACTIONr_mcangle_it1.5661.8651597
X-RAY DIFFRACTIONr_mcangle_other1.5661.8671598
X-RAY DIFFRACTIONr_scbond_it1.6851.5671455
X-RAY DIFFRACTIONr_scbond_other1.5621.5291401
X-RAY DIFFRACTIONr_scangle_it2.1872.2682075
X-RAY DIFFRACTIONr_scangle_other1.9782.1982003
X-RAY DIFFRACTIONr_lrange_it4.00618.0453273
X-RAY DIFFRACTIONr_lrange_other2.99316.0333078
X-RAY DIFFRACTIONr_rigid_bond_restr1.48835304
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.05-1.0770.3665370.369103760.368115330.0870.0994.62410.365
1.077-1.1070.3065510.32105000.319112830.6040.697.94380.32
1.107-1.1390.2735400.271102710.271109860.8130.81798.40710.269
1.139-1.1740.2375270.24199520.241106390.8810.87498.49610.232
1.174-1.2120.2365090.21897440.219103860.8890.89298.71940.206
1.212-1.2550.2014870.19994250.199100230.9170.91498.89250.183
1.255-1.3020.1824560.17191270.17196620.9340.93599.18240.151
1.302-1.3550.1654860.14587320.14692720.9490.95599.41760.122
1.355-1.4160.1534380.12584920.12789710.9590.96699.5430.105
1.416-1.4850.1424390.1181150.11285810.9690.97599.68540.092
1.485-1.5650.1224230.09577180.09681670.9790.98499.68160.078
1.565-1.660.1284100.08873380.0977530.9790.98699.93550.074
1.66-1.7740.123620.08969060.09172730.9830.98699.93130.076
1.774-1.9160.1163140.0964770.09167910.9850.9881000.079
1.916-2.0990.1212880.09959760.162660.9840.98799.96810.09
2.099-2.3460.122810.09454410.09557220.9840.9881000.085
2.346-2.7080.1252550.10348040.10550590.9830.9841000.093
2.708-3.3150.1412270.12441050.12543330.9790.9899.97690.117
3.315-4.6780.1531680.12132320.12234000.980.9831000.122
4.678-52.5450.274840.23719140.23819990.9590.95799.950.244

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