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- PDB-1j54: Structure of the N-terminal exonuclease domain of the epsilon sub... -

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Basic information

Entry
Database: PDB / ID: 1j54
TitleStructure of the N-terminal exonuclease domain of the epsilon subunit of E.coli DNA polymerase III at pH 5.8
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: 1.7 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_alt_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_alt_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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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: DNA polymerase III, epsilon chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3607
Polymers20,7421
Non-polymers6186
Water4,053225
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
Components on special symmetry positions
IDModelComponents
11A-6178-

HOH

21A-6184-

HOH

31A-6204-

HOH

41A-6207-

HOH

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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.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG 8000, magnesium sulfate, cacodylate, pH 5.8, 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: 1.7→50 Å / Num. obs: 22532 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.8 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 9
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.152 / Num. unique all: 1813 / % possible all: 78
Reflection
*PLUS
Rmerge(I) obs: 0.049
Reflection shell
*PLUS
Rmerge(I) obs: 0.152

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
CNSrefinement
CCP4phasing
RefinementResolution: 1.7→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)
RfactorNum. reflection% reflection
Rfree0.234 1179 -
Rwork0.201 --
obs-22457 94.9 %
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1360 0 56 225 1641
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.339
Refinement
*PLUS
Rfactor Rfree: 0.234 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS

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