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- PDB-2nq9: High resolution crystal structure of Escherichia coli endonucleas... -

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Basic information

Entry
Database: PDB / ID: 2nq9
TitleHigh resolution crystal structure of Escherichia coli endonuclease IV (Endo IV) Y72A mutant bound to damaged DNA
Components
  • 5'-D(*AP*TP*AP*TP*CP*T)-3'
  • 5'-D(*AP*TP*CP*TP*GP*AP*AP*GP*TP*AP*T)-3'
  • 5'-D(P*(3DR)P*AP*GP*AP*T)-3'
  • Endonuclease 4
KeywordsHYDROLASE/DNA / TIM-barrel / trinuclear Zn active site / HYDROLASE-DNA COMPLEX
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 / 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
DNA / DNA (> 10) / Endonuclease 4
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*AP*TP*AP*TP*CP*T)-3'
C: 5'-D(P*(3DR)P*AP*GP*AP*T)-3'
D: 5'-D(*AP*TP*CP*TP*GP*AP*AP*GP*TP*AP*T)-3'
A: Endonuclease 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1737
Polymers37,9774
Non-polymers1963
Water6,233346
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.500, 59.100, 51.200
Angle α, β, γ (deg.)90.00, 94.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

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DNA chain , 3 types, 3 molecules BCD

#1: DNA chain 5'-D(*AP*TP*AP*TP*CP*T)-3'


Mass: 1783.216 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(P*(3DR)P*AP*GP*AP*T)-3'


Mass: 1394.951 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(*AP*TP*CP*TP*GP*AP*AP*GP*TP*AP*T)-3'


Mass: 3372.234 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 1 molecules A

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


Mass: 31426.402 Da / Num. of mol.: 1 / Mutation: Y72A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nfo / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): nfo- strain BW565DE3 / References: UniProt: P0A6C1, deoxyribonuclease IV

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Non-polymers , 2 types, 349 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% MPEG-2000, 0.1 M HEPES pH 7, and 0.4 M 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: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 10, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.41→20 Å / Num. obs: 78368 / % possible obs: 98 % / Observed criterion σ(I): 278343 / Rsym value: 0.098 / Net I/σ(I): 18.3

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Processing

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

1qtw


Resolution: 1.45→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.234 3689 -
Rwork0.22 --
obs-72836 5 %
Displacement parametersBiso mean: 16.63 Å2
Refinement stepCycle: LAST / Resolution: 1.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 438 3 346 2953
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0038
X-RAY DIFFRACTIONc_angle_d1.093
LS refinement shellResolution: 1.45→1.54 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.248 618 -
Rwork0.229 --
obs-11494 99.9 %

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