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- PDB-1j53: Structure of the N-terminal Exonuclease Domain of the Epsilon Sub... -

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Basic information

Entry
Database: PDB / ID: 1j53
TitleStructure of the N-terminal Exonuclease Domain of the Epsilon Subunit of E.coli DNA Polymerase III at pH 8.5
ComponentsDNA polymerase III, epsilon chain
KeywordsTRANSFERASE / DNA polymerase proofreading domain
Function / homology
Function and homology information


DNA polymerase III, core complex / DNA polymerase III complex / DNA replication proofreading / 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 polymerase III complex / DNA replication proofreading / 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
: / THYMIDINE-5'-PHOSPHATE / DNA polymerase III subunit epsilon
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsHamdan, S. / Carr, P.D. / Brown, S.E. / Ollis, D.L. / Dixon, N.E.
CitationJournal: Structure / Year: 2002
Title: Structural Basis for Proofreading during Replication of the Escherichia coli Chromosome
Authors: Hamdan, S. / Carr, P.D. / Brown, S.E. / Ollis, D.L. / Dixon, N.E.
History
DepositionJan 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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.pdbx_leaving_atom_flag / _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
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase III, epsilon chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6207
Polymers20,7421
Non-polymers8786
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.8, 60.8, 111.1
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DNA polymerase III, epsilon chain


Mass: 20741.689 Da / Num. of mol.: 1 / Fragment: N-terminal exonuclease domain (residues 1-186)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PSHSH1018 / Genus (production host): T7-like viruses / Production host: Enterobacteria phage T7 (virus) / References: UniProt: P03007, DNA-directed DNA polymerase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N2O8P
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, magnesium sulfate, cacodylate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Details: Hamdan, S., (2000) J.Struct.Biol., 131, 164.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMsodium HEPES1droppH7.5
22 mMdithiothreitol1drop
311.5 mg/mlprotein1drop
45 mMTMP1drop
55 mM1dropMnSO4
620-21 %PEG80001reservoir
70.1 Mcacodylate1reservoirpH5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9796
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 5, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 20091 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.1 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 6.8
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.204 / Num. unique all: 1920 / % possible all: 98.4
Reflection
*PLUS
Rmerge(I) obs: 0.041
Reflection shell
*PLUS
Rmerge(I) obs: 0.204

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
CNSrefinement
CCP4phasing
RefinementResolution: 1.8→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: maximum likelihood target refinements (positional, individual B-factor, and simulated annealing using standard CNS scripts). The TMP 2100 molecule was fitted into the electron density but ...Details: maximum likelihood target refinements (positional, individual B-factor, and simulated annealing using standard CNS scripts). The TMP 2100 molecule was fitted into the electron density but not refined (as attempts to do so increased the Rfree value). The occupancies are zero.
RfactorNum. reflection% reflection
Rfree0.227 1021 -
Rwork0.199 --
obs-19726 98.2 %
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1360 0 52 229 1641
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.265
Refinement
*PLUS
Rfactor Rfree: 0.227 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS

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