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Basic information

Entry
Database: PDB / ID: 2gui
TitleStructure and Function of Cyclized Versions of the Proofreading Exonuclease Subunit of E. coli DNA Polymerase III
ComponentsDNA polymerase III epsilon subunit
KeywordsTRANSFERASE / DNA polymerase proofreading domain
Function / homology
Function and homology information


DNA polymerase III, core complex / DNA replication proofreading / DNA polymerase III complex / lagging strand elongation / replisome / exonuclease activity / leading strand elongation / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase ...DNA polymerase III, core complex / DNA replication proofreading / DNA polymerase III complex / lagging strand elongation / replisome / exonuclease activity / leading strand elongation / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / metal ion binding / cytosol
Similarity search - Function
DNA polymerase 3, epsilon subunit / DNA polymerase III epsilon subunit, exonuclease domain / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / URIDINE-5'-MONOPHOSPHATE / DNA polymerase III subunit epsilon
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsPark, A.Y. / Carr, P.D. / Ollis, D.L. / Dixon, N.E.
CitationJournal: To be Published
Title: Structure and Function of Cyclized Versions of the Proofreading Exonuclease Subunit E. coli DNA Polymerase III
Authors: Park, A.Y. / Carr, P.D. / Oliis, D.L. / Dixon, N.E.
History
DepositionApr 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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
Remark 999SEQUENCE The protein is a cyclized form of N-terminal domain of epsilon (residue 2-186). The ...SEQUENCE The protein is a cyclized form of N-terminal domain of epsilon (residue 2-186). The cyclized protein includes 9 amino acid linker, SIEF at the N-terminal and TRESG at the C-terminus

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase III epsilon subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6078
Polymers21,6191
Non-polymers9887
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.099, 60.099, 109.164
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-5110-

HOH

21A-5132-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase III epsilon subunit


Mass: 21618.559 Da / Num. of mol.: 1 / Fragment: N-terminal exonuclease domain, residues 2-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaQ, mutD / Plasmid: pGL1182 / Production host: Escherichia coli (E. coli) / References: UniProt: P03007, DNA-directed DNA polymerase

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Non-polymers , 5 types, 247 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE / Uridine monophosphate


Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.1 M Cacodylate Acid, 20% PEG-8K, 2.5 mM UMP, 5 mM MnSO4, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1.128 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 11, 2004
RadiationMonochromator: Si(III) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.128 Å / Relative weight: 1
ReflectionResolution: 1.6→26.9 Å / Num. obs: 27900 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.058 / Net I/σ(I): 9
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 4.97 / Num. unique all: 2618 / % possible all: 96.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1J53

1j53


Resolution: 1.6→26.88 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.244 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19746 1366 5 %RANDOM
Rwork0.16016 ---
all0.16195 ---
obs0.16195 25755 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.751 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→26.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1368 0 50 240 1658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221503
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.9812042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.815189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41224.20369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.73215245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.647159
X-RAY DIFFRACTIONr_chiral_restr0.0780.2231
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021135
X-RAY DIFFRACTIONr_nbd_refined0.2060.2864
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21092
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2252
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.231
X-RAY DIFFRACTIONr_mcbond_it0.7181.5927
X-RAY DIFFRACTIONr_mcangle_it1.18521474
X-RAY DIFFRACTIONr_scbond_it1.9183622
X-RAY DIFFRACTIONr_scangle_it3.0854.5568
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 96 -
Rwork0.195 1837 -
all-1933 -
obs--98.02 %

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