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- PDB-3zd8: Potassium bound structure of E. coli ExoIX in P1 -

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Basic information

Entry
Database: PDB / ID: 3zd8
TitlePotassium bound structure of E. coli ExoIX in P1
ComponentsPROTEIN XNI
KeywordsHYDROLASE / 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
: / Flap endonuclease Xni
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsAnstey-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.
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 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_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.ptnr2_symmetry / _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: PROTEIN XNI
B: PROTEIN XNI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4854
Polymers56,4062
Non-polymers782
Water4,450247
1
A: PROTEIN XNI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2422
Polymers28,2031
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PROTEIN XNI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2422
Polymers28,2031
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.370, 56.554, 60.489
Angle α, β, γ (deg.)110.35, 95.26, 94.88
Int Tables number1
Space group name H-MP1

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Components

#1: Protein PROTEIN XNI / EXOIX


Mass: 28203.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: XL1 BLUE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PCI857
References: UniProt: Q8X6R9, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: STRUCTURE SOLVED USING MERCURY SULPHATE AND GOLD CYANIDE DERIVATIVES COLLECTED IN HOUSE
Crystal growpH: 6.5
Details: 0.2 M SODIUM THIOCYANATE, 20% PEG 3350, 0.1 M MES AT PH 6.5

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 0.870, 1.542, 1.542
DetectorType: ADSC QUANTUM Q4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.871
21.5421
ReflectionResolution: 2→20 Å / Num. obs: 34557 / % possible obs: 92.3 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 8.8
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.1 / % possible all: 80.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR
Starting model: NONE

Resolution: 2→18.22 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.292 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22719 1708 5.1 %RANDOM
Rwork0.15993 ---
obs0.16339 31471 92.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.815 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2---0.01 Å20.03 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→18.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3723 0 2 247 3972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223812
X-RAY DIFFRACTIONr_bond_other_d0.0010.022558
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.9515183
X-RAY DIFFRACTIONr_angle_other_deg0.98636236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2335472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92923.873173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25115622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4341526
X-RAY DIFFRACTIONr_chiral_restr0.1020.2582
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214232
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02748
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_it23.0351.52384
X-RAY DIFFRACTIONr_mcbond_other4.111.5954
X-RAY DIFFRACTIONr_mcangle_it23.35823822
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it80.96531428
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it65.264.51361
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→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 109 -
Rwork0.242 2014 -
obs--80.85 %

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