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- PDB-4k1g: Structure of E. coli Nfo(Endo IV)-H69A mutant bound to a cleaved ... -

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Basic information

Entry
Database: PDB / ID: 4k1g
TitleStructure of E. coli Nfo(Endo IV)-H69A mutant bound to a cleaved DNA duplex containing a alphadA:T basepair
Components
  • DNA (5'-D(*CP*GP*TP*CP*GP*TP*CP*GP*TP*GP*GP*AP*CP*GP*C)-3')
  • DNA (5'-D(*GP*CP*GP*TP*CP*C)-3')
  • DNA (5'-D(P*AP*CP*GP*AP*CP*GP*AP*CP*G)-3')
  • Endonuclease 4
KeywordsHYDROLASE/DNA / DNA endonuclease IV / HYDROLASE-DNA complex
Function / homology
Function and homology information


deoxyribonuclease IV / deoxyribonuclease IV (phage-T4-induced) activity / phosphoric diester hydrolase activity / 3'-5'-DNA exonuclease 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 / phosphoric diester hydrolase activity / 3'-5'-DNA exonuclease 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 2 / AP endonuclease family 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 2 / AP endonuclease family 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
DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / Endonuclease 4
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMorera, S. / Vigouroux, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Insight into mechanisms of 3'-5' exonuclease activity and removal of bulky 8,5'-cyclopurine adducts by apurinic/apyrimidinic endonucleases.
Authors: Mazouzi, A. / Vigouroux, A. / Aikeshev, B. / Brooks, P.J. / Saparbaev, M.K. / Morera, S. / Ishchenko, A.A.
History
DepositionApr 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
E: DNA (5'-D(*GP*CP*GP*TP*CP*C)-3')
F: DNA (5'-D(*CP*GP*TP*CP*GP*TP*CP*GP*TP*GP*GP*AP*CP*GP*C)-3')
H: DNA (5'-D(P*AP*CP*GP*AP*CP*GP*AP*CP*G)-3')
M: DNA (5'-D(*GP*CP*GP*TP*CP*C)-3')
N: DNA (5'-D(*CP*GP*TP*CP*GP*TP*CP*GP*TP*GP*GP*AP*CP*GP*C)-3')
O: DNA (5'-D(P*AP*CP*GP*AP*CP*GP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,71615
Polymers81,1778
Non-polymers5397
Water10,989610
1
A: Endonuclease 4
E: DNA (5'-D(*GP*CP*GP*TP*CP*C)-3')
F: DNA (5'-D(*CP*GP*TP*CP*GP*TP*CP*GP*TP*GP*GP*AP*CP*GP*C)-3')
H: DNA (5'-D(P*AP*CP*GP*AP*CP*GP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8918
Polymers40,5884
Non-polymers3024
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-118 kcal/mol
Surface area15800 Å2
MethodPISA
2
B: Endonuclease 4
M: DNA (5'-D(*GP*CP*GP*TP*CP*C)-3')
N: DNA (5'-D(*CP*GP*TP*CP*GP*TP*CP*GP*TP*GP*GP*AP*CP*GP*C)-3')
O: DNA (5'-D(P*AP*CP*GP*AP*CP*GP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8257
Polymers40,5884
Non-polymers2373
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-92 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.950, 136.660, 112.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsAUTHORS STATE THAT THE QUATERNARY STRUCTURE IS A PROTEIN MONOMER-DOUBLE STRANDED DNA COMPLEX. ONE OF THE DNA STRANDS IS CLEAVED BETWEEN THE BASE 306 AND THE BASE 307.

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 31451.430 Da / Num. of mol.: 2 / Mutation: H69A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: nfo, b2159, JW2146 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6C1, deoxyribonuclease IV

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DNA chain , 3 types, 6 molecules EMFNHO

#2: DNA chain DNA (5'-D(*GP*CP*GP*TP*CP*C)-3')


Mass: 1785.193 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*CP*GP*TP*CP*GP*TP*CP*GP*TP*GP*GP*AP*CP*GP*C)-3')


Mass: 4601.971 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: DNA chain DNA (5'-D(P*AP*CP*GP*AP*CP*GP*AP*CP*G)-3')


Mass: 2749.826 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 3 types, 617 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsCHAINS E AND H, AND CHAINS M AND O ARE FORM THE SAME DNA STRAND WHICH IS CLEAVED BETWEEN THE BASE ...CHAINS E AND H, AND CHAINS M AND O ARE FORM THE SAME DNA STRAND WHICH IS CLEAVED BETWEEN THE BASE 306 AND THE BASE 307.

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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: 2.79 Å3/Da / Density % sol: 55.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, Tris HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 20, 2011
RadiationMonochromator: SiIII / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→41.5 Å / Num. all: 71040 / Num. obs: 71003 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Biso Wilson estimate: 26.58 Å2
Reflection shellResolution: 1.9→2.02 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2NQJ

2nqj


Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.9455 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2123 3550 5 %RANDOM
Rwork0.1762 ---
obs0.178 70976 99.13 %-
all-71003 --
Displacement parametersBiso mean: 31.25 Å2
Baniso -1Baniso -2Baniso -3
1-6.8084 Å20 Å20 Å2
2---3.4576 Å20 Å2
3----3.3507 Å2
Refine analyzeLuzzati coordinate error obs: 0.199 Å
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4366 1182 19 610 6177
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015827HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.128129HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2248SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes122HARMONIC2
X-RAY DIFFRACTIONt_gen_planes728HARMONIC5
X-RAY DIFFRACTIONt_it5827HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion17.98
X-RAY DIFFRACTIONt_chiral_improper_torsion779SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6808SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2423 232 5.01 %
Rwork0.219 4396 -
all0.2201 4628 -
obs--99.13 %

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