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- PDB-3zdc: Structure of E. coli ExoIX in complex with the palindromic 5ov4 D... -

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Basic information

Entry
Database: PDB / ID: 3zdc
TitleStructure of E. coli ExoIX in complex with the palindromic 5ov4 DNA oligonucleotide, potassium and calcium
Components
  • 5OV4 DNA, 5'-D(*AP*AP*AP*AP*GP*CP*GP*TP*AP*CP*GP*CP)-3'
  • PROTEIN XNI
KeywordsHYDROLASE / EXOIX / FLAP ENDONUCLEASE / DNA BINDING
Function / homology
Function and homology information


DNA replication, Okazaki fragment processing / 5'-flap endonuclease activity / 5'-3' exonuclease activity / potassium ion binding / Hydrolases; Acting on ester bonds / magnesium ion binding / DNA binding
Similarity search - Function
Flap endonuclease Xni / Flap endonuclease / 5'-nuclease / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Helix-hairpin-helix motif, class 2 ...Flap endonuclease Xni / Flap endonuclease / 5'-nuclease / DNA polymerase I-like, H3TH domain / 5'-3' exonuclease, C-terminal SAM fold / 5'-3' exonuclease, alpha-helical arch, N-terminal / 5'-3' exonuclease, N-terminal resolvase-like domain / 5'-3' exonuclease / 5'-3' exonuclease / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / DNA / DNA (> 10) / Flap endonuclease Xni
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsHemsworth, G.R. / Anstey-Gilbert, C.S. / Flemming, C.S. / Hodskinson, M.R.G. / Zhang, J. / Sedelnikova, S.E. / Stillman, T.J. / Sayers, J.R. / Artymiuk, P.J.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: The Structure of E. Coli Exoix - Implications for DNA Binding and Catalysis in Flap Endonucleases
Authors: Anstey-Gilbert, C.S. / Hemsworth, G.R. / Flemming, C.S. / Hodskinson, M.R.G. / Zhang, J. / Sedelnikova, S.E. / Stillman, T.J. / Sayers, J.R. / Artymiuk, P.J.
History
DepositionNov 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_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_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

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Assembly

Deposited unit
A: PROTEIN XNI
X: 5OV4 DNA, 5'-D(*AP*AP*AP*AP*GP*CP*GP*TP*AP*CP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1217
Polymers31,8842
Non-polymers2375
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-31.5 kcal/mol
Surface area14230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.178, 152.688, 34.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / DNA chain , 2 types, 2 molecules AX

#1: Protein PROTEIN XNI / EXOIX


Mass: 28203.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: XL1 BLUE / Plasmid: PJONEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8X6R9, Hydrolases; Acting on ester bonds
#2: DNA chain 5OV4 DNA, 5'-D(*AP*AP*AP*AP*GP*CP*GP*TP*AP*CP*GP*CP)-3'


Mass: 3680.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 4 types, 164 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsOLIGO DESIGNED BASED ON INITIAL STRUCTURE WITH FRAGMENT OF LARGER DNA

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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: 60 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.2 M CALCIUM ACETATE, 15% (W/V) PEG-3350, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2009 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.53→40 Å / Num. obs: 53386 / % possible obs: 97.9 % / Observed criterion σ(I): 6 / Redundancy: 4.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.7
Reflection shellResolution: 1.53→1.61 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.2 / % possible all: 97.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EXOIX FLAP1 FRAGMENT COMPLEX STRUCTURE

Resolution: 1.53→34.53 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.321 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22865 2697 5.1 %RANDOM
Rwork0.20485 ---
obs0.20603 50688 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å20 Å20 Å2
2--0.47 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.53→34.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1897 245 11 159 2312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212228
X-RAY DIFFRACTIONr_bond_other_d0.0010.021400
X-RAY DIFFRACTIONr_angle_refined_deg1.4292.0983082
X-RAY DIFFRACTIONr_angle_other_deg0.93133428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5315247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.58523.76585
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73215309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0391513
X-RAY DIFFRACTIONr_chiral_restr0.0860.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212316
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02408
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it9.5931.51241
X-RAY DIFFRACTIONr_mcbond_other1.0191.5495
X-RAY DIFFRACTIONr_mcangle_it11.02621980
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it16.6713987
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it17.6884.51101
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.532→1.572 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 191 -
Rwork0.31 3624 -
obs--96.66 %

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