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- PDB-2ido: Structure of the E. coli Pol III epsilon-Hot proofreading complex -

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Basic information

Entry
Database: PDB / ID: 2ido
TitleStructure of the E. coli Pol III epsilon-Hot proofreading complex
Components
  • DNA polymerase III epsilon subunit
  • Hot protein
KeywordsTRANSFERASE / Polymerase / exonuclease / Hot / epsilon / Pol III
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 replication ...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 replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / THYMIDINE-5'-PHOSPHATE / DNA polymerase III subunit epsilon / Hot
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Enterobacteria phage (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKirby, T.W. / Harvey, S. / DeRose, E.F. / Chalov, S. / Chikova, A.K. / Perrino, F.W. / Schaaper, R.M. / London, R.E. / Pedersen, L.C.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure of the Escherichia coli DNA polymerase III epsilon-HOT proofreading complex.
Authors: Kirby, T.W. / Harvey, S. / DeRose, E.F. / Chalov, S. / Chikova, A.K. / Perrino, F.W. / Schaaper, R.M. / London, R.E. / Pedersen, L.C.
History
DepositionSep 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 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.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

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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
B: Hot protein
C: DNA polymerase III epsilon subunit
D: Hot protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,88412
Polymers60,9034
Non-polymers9818
Water7,728429
1
A: DNA polymerase III epsilon subunit
B: Hot protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8845
Polymers30,4522
Non-polymers4323
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-31 kcal/mol
Surface area12590 Å2
MethodPISA
2
C: DNA polymerase III epsilon subunit
D: Hot protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0017
Polymers30,4522
Non-polymers5495
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-33 kcal/mol
Surface area12690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.289, 77.289, 212.978
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11C-2155-

HOH

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein DNA polymerase III epsilon subunit


Mass: 20741.689 Da / Num. of mol.: 2 / Fragment: exonuclease domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaQ, mutD / Plasmid: pOXO4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03007, DNA-directed DNA polymerase
#2: Protein Hot protein


Mass: 9709.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage (virus) / Genus: P1-like viruses / Strain: P1 / Gene: hot / Plasmid: PET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BLR(DE3) / References: UniProt: Q71T70

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Non-polymers , 4 types, 437 molecules

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


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


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Crystals grown in .1M Tris, 5mM MnSO4, 5mM dTMP, and 22% PEG6000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Jan 27, 2006 / Details: VariMax
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 38546 / Num. obs: 37506 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 17.5
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2890 / Rsym value: 0.328 / % possible all: 76.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J53

1j53


Resolution: 2.1→24.76 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 282736.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 3522 10 %RANDOM
Rwork0.206 ---
all0.209 38819 --
obs0.209 35297 91.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.0083 Å2 / ksol: 0.316647 e/Å3
Displacement parametersBiso mean: 31.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.23 Å20 Å2
3---0.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3959 0 51 429 4439
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it2.942.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.316 458 9.9 %
Rwork0.269 4150 -
obs--73.1 %
Xplor fileSerial no: 1 / Param file: all.param / Topol file: all.top

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