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- PDB-2nqj: Crystal structure of Escherichia coli endonuclease IV (Endo IV) E... -

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Basic information

Entry
Database: PDB / ID: 2nqj
TitleCrystal structure of Escherichia coli endonuclease IV (Endo IV) E261Q mutant bound to damaged DNA
Components
  • 5'-D(*CP*GP*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*GP*C)-3'
  • 5'-D(*GP*CP*GP*TP*CP*CP*(3DR)P*CP*GP*AP*CP*GP*AP*CP*G)-3'
  • Endonuclease 4
KeywordsHYDROLASE / Tim_barrel / trinuclear zinc site
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
DNA / DNA (> 10) / Endonuclease 4
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsGarcin-Hosfield, E.D. / Hosfield, D.J. / Tainer, J.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: DNA apurinic-apyrimidinic site binding and excision by endonuclease IV.
Authors: Garcin, E.D. / Hosfield, D.J. / Desai, S.A. / Haas, B.J. / Bjoras, M. / Cunningham, R.P. / Tainer, J.A.
History
DepositionOct 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). ALTHOUGH CHAIN B COULD BE MOVED BY A SYMMETRY OPERATION, THE COMPLEX FORMED BY CHAIN B WITH CHAIN C AND D IS NOT BIOLOGICALLY RELEVANT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*GP*CP*GP*TP*CP*CP*(3DR)P*CP*GP*AP*CP*GP*AP*CP*G)-3'
D: 5'-D(*CP*GP*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*GP*C)-3'
A: Endonuclease 4
B: Endonuclease 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3718
Polymers72,1094
Non-polymers2624
Water5,855325
1
C: 5'-D(*GP*CP*GP*TP*CP*CP*(3DR)P*CP*GP*AP*CP*GP*AP*CP*G)-3'
D: 5'-D(*CP*GP*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*GP*C)-3'
A: Endonuclease 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7886
Polymers40,5913
Non-polymers1963
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endonuclease 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5832
Polymers31,5181
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.6, 86.2, 148.3
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain 5'-D(*GP*CP*GP*TP*CP*CP*(3DR)P*CP*GP*AP*CP*GP*AP*CP*G)-3'


Mass: 4446.864 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*GP*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*GP*C)-3'


Mass: 4626.984 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Endonuclease 4 / Endonuclease IV / Endodeoxyribonuclease IV


Mass: 31517.512 Da / Num. of mol.: 2 / Mutation: E261Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: nfo- strain BW565DE3 / Gene: nfo / Plasmid: pET24 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A6C1, deoxyribonuclease IV
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% MPEG-2000, 0.1M HEPES pH 7, 0.4M sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MPEG-200011
2HEPES11
3sodium acetate11
4MPEG-200012
5HEPES12
6sodium acetate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 10, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. obs: 24943 / % possible obs: 93 % / Rsym value: 0.095 / Net I/σ(I): 14.6

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QTW

1qtw


Resolution: 2.45→20 Å / σ(F): 0
RfactorNum. reflection
Rfree0.254 1252
Rwork0.198 -
obs-24906
Solvent computationBsol: 50.958 Å2
Displacement parametersBiso mean: 36.078 Å2
Baniso -1Baniso -2Baniso -3
1--19.744 Å20 Å20 Å2
2--13.221 Å20 Å2
3---6.523 Å2
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4346 601 4 325 5276
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.143
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3param19x.zn
X-RAY DIFFRACTION4CNS_TOPPAR:dna-rna_rep.param

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