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- PDB-8rly: E. coli endonuclease IV complexed with sulfate, catalytic Fe2+ -

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Basic information

Entry
Database: PDB / ID: 8rly
TitleE. coli endonuclease IV complexed with sulfate, catalytic Fe2+
ComponentsEndonuclease 4
KeywordsDNA BINDING PROTEIN / bacterial endonuclease IV / catalytic iron
Function / homology
Function and homology information


deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / 3'-5'-DNA exonuclease activity / phosphoric diester hydrolase activity / phosphatase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / endonuclease activity / DNA repair / DNA binding ...deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / 3'-5'-DNA exonuclease activity / phosphoric diester hydrolase activity / phosphatase activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / base-excision repair / endonuclease activity / DNA repair / DNA binding / zinc ion binding / cytosol
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 / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
: / NICKEL (II) ION / Endonuclease 4
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSaper, M.A. / Paterson, N.G. / Kirillov, S. / Rouvinski, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Biochemistry / Year: 2025
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.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJan 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 25, 2024Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 15, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endonuclease 4
B: Endonuclease 4
C: Endonuclease 4
D: Endonuclease 4
E: Endonuclease 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,83338
Polymers157,5925
Non-polymers2,24033
Water20,1411118
1
A: Endonuclease 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1699
Polymers31,5181
Non-polymers6518
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endonuclease 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9548
Polymers31,5181
Non-polymers4367
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endonuclease 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9548
Polymers31,5181
Non-polymers4367
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endonuclease 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8606
Polymers31,5181
Non-polymers3415
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Endonuclease 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8957
Polymers31,5181
Non-polymers3776
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.780, 115.980, 177.700
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, 5 molecules ABCDE

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


Mass: 31518.496 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: C-terminus not resolved in some of the chains. / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nfo, b2159, JW2146 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BH110(DE3) / References: UniProt: P0A6C1, deoxyribonuclease IV

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Non-polymers , 7 types, 1151 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1118 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 1 microliter protein mixed with 2 microliter precipitant. Protein: 12.5 mg/ml, 20 mM Tris-HCl pH 8.0, 150 mM NaCl. Precipitant: 0.1 M HEPES pH 7.0, 15% Polyethylene Glycol 3,350, 10 mM ...Details: 1 microliter protein mixed with 2 microliter precipitant. Protein: 12.5 mg/ml, 20 mM Tris-HCl pH 8.0, 150 mM NaCl. Precipitant: 0.1 M HEPES pH 7.0, 15% Polyethylene Glycol 3,350, 10 mM Magnesium chloride hexahydrate, 5 mM nickel (II) chloride hexahydrate

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11701N
21701N
31701N
41701N
51701N
61701N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0311.7712
SYNCHROTRONDiamond I0321.6984
SYNCHROTRONDiamond I0331.5028
SYNCHROTRONDiamond I0341.476
SYNCHROTRONDiamond I0351.3051
SYNCHROTRONDiamond I0361.2782
Detector
TypeIDDetectorDate
DECTRIS EIGER X 16M1PIXELNov 29, 2023
DECTRIS EIGER X 16M2PIXELNov 29, 2023
DECTRIS EIGER X 16M3PIXELNov 29, 2023
DECTRIS EIGER X 16M4PIXELNov 29, 2023
DECTRIS EIGER X 16M5PIXELNov 29, 2023
DECTRIS EIGER X 16M6PIXELNov 29, 2023
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
4SINGLE WAVELENGTHMx-ray4
5SINGLE WAVELENGTHMx-ray5
6SINGLE WAVELENGTHMx-ray6
Radiation wavelength
IDWavelength (Å)Relative weight
11.77121
21.69841
31.50281
41.4761
51.30511
61.27821
ReflectionResolution: 1.9→97.12 Å / Num. obs: 193287 / % possible obs: 87.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 22.18 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06475 / Rrim(I) all: 0.07067 / Net I/av σ(I): 14.86 / Net I/σ(I): 14.86
Reflection shellResolution: 1.9→1.92 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.3256 / Mean I/σ(I) obs: 1.36 / Num. unique obs: 372 / CC1/2: 0.772 / Rpim(I) all: 0.3083 / Rrim(I) all: 0.4496 / % possible all: 21.7

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Processing

Software
NameVersionClassification
PHENIX1.21_5190refinement
xia23.17.0data reduction
Aimlessdata scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QTW

1qtw


Resolution: 1.9→97.12 Å / SU ML: 0.1741 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.4556
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2068 9776 5.07 %
Rwork0.1565 182902 -
obs0.159 192678 87.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.66 Å2
Refinement stepCycle: LAST / Resolution: 1.9→97.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10994 0 67 1118 12179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009611274
X-RAY DIFFRACTIONf_angle_d0.967415256
X-RAY DIFFRACTIONf_chiral_restr0.05561670
X-RAY DIFFRACTIONf_plane_restr0.01131997
X-RAY DIFFRACTIONf_dihedral_angle_d14.29394047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.255880.2741504X-RAY DIFFRACTION21.72
1.92-1.940.32011170.2512259X-RAY DIFFRACTION32.6
1.94-1.970.29471590.22653063X-RAY DIFFRACTION44.06
1.97-1.990.27561670.20893885X-RAY DIFFRACTION54.76
1.99-2.020.25552530.19944373X-RAY DIFFRACTION63.81
2.02-2.050.24172800.18224967X-RAY DIFFRACTION71.45
2.05-2.080.23362870.17375485X-RAY DIFFRACTION79.35
2.08-2.110.24712800.1715986X-RAY DIFFRACTION85.26
2.11-2.140.233520.16636463X-RAY DIFFRACTION93.18
2.14-2.170.21033870.15566632X-RAY DIFFRACTION95.59
2.18-2.210.20873730.14996753X-RAY DIFFRACTION97.64
2.21-2.250.22083610.15986730X-RAY DIFFRACTION96.49
2.25-2.30.20793720.15726879X-RAY DIFFRACTION99.68
2.3-2.340.22543460.15736831X-RAY DIFFRACTION98.59
2.34-2.390.21714000.15546918X-RAY DIFFRACTION99.62
2.39-2.450.23313660.16356929X-RAY DIFFRACTION99.51
2.45-2.510.23063680.16247000X-RAY DIFFRACTION99.88
2.51-2.580.21293920.15726884X-RAY DIFFRACTION99.99
2.58-2.650.21343750.16026934X-RAY DIFFRACTION99.99
2.65-2.740.20293420.16186928X-RAY DIFFRACTION100
2.74-2.840.22064120.16426940X-RAY DIFFRACTION100
2.84-2.950.22233920.17256952X-RAY DIFFRACTION99.99
2.95-3.090.22363610.17736916X-RAY DIFFRACTION100
3.09-3.250.23263360.17266988X-RAY DIFFRACTION99.99
3.25-3.450.20823790.16146943X-RAY DIFFRACTION99.99
3.45-3.720.18973080.1467018X-RAY DIFFRACTION99.95
3.72-4.090.18884230.1326917X-RAY DIFFRACTION99.97
4.09-4.690.14433190.11756981X-RAY DIFFRACTION100
4.69-5.90.17574000.14066929X-RAY DIFFRACTION100
5.9-97.120.18293810.15566915X-RAY DIFFRACTION99.81

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