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- PDB-3zde: Potassium free structure of E. coli ExoIX -

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Basic information

Entry
Database: PDB / ID: 3zde
TitlePotassium free structure of E. coli ExoIX
ComponentsPROTEIN XNI
KeywordsHYDROLASE / 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
Flap endonuclease Xni
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN XNI


Theoretical massNumber of molelcules
Total (without water)28,2031
Polymers28,2031
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.451, 37.432, 66.698
Angle α, β, γ (deg.)90.00, 117.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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) / Variant (production host): PCI857
References: UniProt: Q8X6R9, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 6.5
Details: 0.2 M SODIUM ACETATE TRIHYDRATE, 20% PEG 3350, pH 6.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.542
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.45→40 Å / Num. obs: 9692 / % possible obs: 92.4 % / Observed criterion σ(I): 6 / Redundancy: 1.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.9
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.4 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EXOIX P21 STRUCTURE

Resolution: 2.45→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.887 / SU B: 9.435 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.657 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.273 474 5.2 %RANDOM
Rwork0.17225 ---
obs0.17728 8558 85.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.536 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å2-0.11 Å2
2--0.85 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 0 0 17 1912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0211939
X-RAY DIFFRACTIONr_bond_other_d0.0010.021292
X-RAY DIFFRACTIONr_angle_refined_deg1.0811.952640
X-RAY DIFFRACTIONr_angle_other_deg0.85833147
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6855242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.55623.88990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4415310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0521514
X-RAY DIFFRACTIONr_chiral_restr0.0590.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212173
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02384
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_it19.8381.51217
X-RAY DIFFRACTIONr_mcbond_other22.2491.5488
X-RAY DIFFRACTIONr_mcangle_it20.20221950
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it23.533722
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it22.6474.5690
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: 2.45→2.581 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.365 66 -
Rwork0.232 1196 -
obs--83.85 %

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