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- PDB-2xy8: Paramagnetic-based NMR structure of the complex between the N- te... -

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Basic information

Entry
Database: PDB / ID: 2xy8
TitleParamagnetic-based NMR structure of the complex between the N- terminal epsilon domain and the theta domain of the DNA polymerase III
Components
  • DNA POLYMERASE III SUBUNIT EPSILON
  • DNA POLYMERASE III SUBUNIT THETA
KeywordsTRANSFERASE / DOCKING / EXPERIMENTAL RESTRAINTS / HADDOCK PROGRAM
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 replication / DNA binding / metal ion binding / cytosol
Similarity search - Function
DNA polymerase III-theta / DNA polymerase III-theta, bacterial / DNA polymerase III-theta superfamily / DNA polymerase III, theta subunit / 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 ...DNA polymerase III-theta / DNA polymerase III-theta, bacterial / DNA polymerase III-theta superfamily / DNA polymerase III, theta subunit / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA polymerase III subunit epsilon / DNA polymerase III subunit theta / DNA polymerase III subunit theta
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodSOLUTION NMR / DATA-DRIVEN FLEXIBLE DOCKING
AuthorsSchmitz, C. / Bonvin, A.M.J.J.
Citation
Journal: J.Biomol.NMR / Year: 2011
Title: Protein-Protein Haddocking Using Exclusively Pseudocontact Shifts.
Authors: Schmitz, C. / Bonvin, A.M.J.J.
#1: Journal: J.Biomol.NMR / Year: 2008
Title: Numbat: An Interactive Software Tool for Fitting Deltachi-Tensors to Molecular Coordinates Using Pseudocontact Shifts
Authors: Schmitz, C. / Stanton-Cook, M.J. / Su, X.C. / Otting, G. / Huber, T.
#2: Journal: J.Am.Chem.Soc. / Year: 2006
Title: Lanthanide Labeling Offers Fast NMR Approach to 3D Structure Determinations of Protein-Protein Complexes
Authors: Pintacuda, G. / Park, A.Y. / Keniry, M.A. / Dixon, N.E. / Otting, G.
#3: Journal: Proteins / Year: 2007
Title: Haddock Versus Haddock: New Features and Performance of Haddock2.0 On the Capri Targets.
Authors: de Vries, S.J. / van Dijk, A.D.J. / Krzeminski, M. / van Dijk, M. / Thureau, A. / Hsu, V. / Wassenaar, T. / Bonvin, A.M.J.J.
History
DepositionNov 16, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Database references / Version format compliance
Revision 1.2Jan 17, 2018Group: Database references / Category: citation / citation_author / Item: _citation.page_last / _citation_author.name
Revision 1.3May 15, 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_nmr_software / pdbx_nmr_spectrometer / 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_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA POLYMERASE III SUBUNIT EPSILON
B: DNA POLYMERASE III SUBUNIT THETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6433
Polymers29,6032
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200TOP 10 STRUCTURES OF THE BEST CLUSTER
RepresentativeModel #1

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Components

#1: Protein DNA POLYMERASE III SUBUNIT EPSILON


Mass: 20741.689 Da / Num. of mol.: 1 / Fragment: EXONUCLEASE DOMAIN, RESIDUES 1-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03007, DNA-directed DNA polymerase
#2: Protein DNA POLYMERASE III SUBUNIT THETA


Mass: 8861.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0ABT0, UniProt: P0ABS8*PLUS, DNA-directed DNA polymerase
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE COMPLEX WAS DOCKED USING PSEUDOCONTACT SHIFT ( PCS) RESTRAINTS.THE CONTENTS OF THE SAMPLE ARE SIMILAR TO THAT DESCRIBED IN LANTHANIDE LABELING OFFERS-FAST NMR APPROACH TO 3D STRUCTRE ...Text: THE COMPLEX WAS DOCKED USING PSEUDOCONTACT SHIFT ( PCS) RESTRAINTS.THE CONTENTS OF THE SAMPLE ARE SIMILAR TO THAT DESCRIBED IN LANTHANIDE LABELING OFFERS-FAST NMR APPROACH TO 3D STRUCTRE DETERMINATIONS OF PROTEIN-PROTEIN COMPLEXES. PINTACUDA ET ALL. JACS 2006

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Sample preparation

Sample conditionspH: 7.2 / Pressure: 1 bar / Temperature: 298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNSA.T.BRUNGER,P.D.ADAMS,G.M.CLORE, W.L.DELANO,P.GROS,R.W.GROSSE-KUNSTLEVE, J.-S.JIANG,J.KUSZEWSKI,M.NILGES,N.S.PANNU, R.J.READ,L.M.RICE,T.SIMONSON,G.L.WARRENrefinement
HADDOCK2.1-PARA BETABETADE VRIESstructure solution
RefinementMethod: DATA-DRIVEN FLEXIBLE DOCKING / Software ordinal: 1
Details: RUNNING WITHIN HADDOCK2.1-PARA BETA. REFINEMENT DETAILS CAN BE FOUND AT THE FOLLOWING PUBLICATION: DE VRIES ET AL. PROTEINS 2007 (REFERENCE 3 IN REMARK 1).
NMR ensembleConformer selection criteria: TOP 10 STRUCTURES OF THE BEST CLUSTER
Conformers calculated total number: 200 / Conformers submitted total number: 10

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