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- PDB-4gx8: Crystal structure of a DNA polymerase III alpha-epsilon chimera -

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Basic information

Entry
Database: PDB / ID: 4gx8
TitleCrystal structure of a DNA polymerase III alpha-epsilon chimera
ComponentsDNA polymerase III subunit epsilon,DNA polymerase III subunit alpha
KeywordsTRANSFERASE / DNA polymerase III / polIII epsilon / polIII alpha / DnaQ / DnaE
Function / homology
Function and homology information


DNA polymerase III, core complex / DNA polymerase III complex / lagging strand elongation / replisome / exonuclease activity / DNA replication proofreading / leading strand elongation / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase ...DNA polymerase III, core complex / DNA polymerase III complex / lagging strand elongation / replisome / exonuclease activity / DNA replication proofreading / 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 / cytoplasm / cytosol
Similarity search - Function
: / : / DNA polymerase III subunit alpha, C-terminal domain / DNA polymerase 3, epsilon subunit / DNA polymerase III epsilon subunit, exonuclease domain / Bacterial DNA polymerase III alpha subunit, thumb domain / DNA polymerase III, alpha subunit / Bacterial DNA polymerase III, alpha subunit, NTPase domain / DNA polymerase, helix-hairpin-helix motif / DNA polymerase III alpha subunit finger domain ...: / : / DNA polymerase III subunit alpha, C-terminal domain / DNA polymerase 3, epsilon subunit / DNA polymerase III epsilon subunit, exonuclease domain / Bacterial DNA polymerase III alpha subunit, thumb domain / DNA polymerase III, alpha subunit / Bacterial DNA polymerase III, alpha subunit, NTPase domain / DNA polymerase, helix-hairpin-helix motif / DNA polymerase III alpha subunit finger domain / Bacterial DNA polymerase III alpha NTPase domain / Helix-hairpin-helix motif / Bacterial DNA polymerase III alpha subunit finger domain / PHP domain / PHP domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Metal-dependent hydrolases / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Nucleic acid-binding, OB-fold / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
DNA polymerase III subunit epsilon / DNA polymerase III subunit alpha
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsRobinson, A. / Horan, N. / Xu, Z.-Q. / Dixon, N.E. / Oakley, A.J.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Proofreading exonuclease on a tether: the complex between the E. coli DNA polymerase III subunits alpha, {varepsilon}, theta and beta reveals a highly flexible arrangement of the proofreading domain
Authors: Ozawa, K. / Horan, N.P. / Robinson, A. / Yagi, H. / Hill, F.R. / Jergic, S. / Xu, Z.Q. / Loscha, K.V. / Li, N. / Tehei, M. / Oakley, A.J. / Otting, G. / Huber, T. / Dixon, N.E.
History
DepositionSep 4, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Jun 21, 2017Group: Advisory / Category: pdbx_distant_solvent_atoms
Revision 1.4Nov 8, 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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,DNA polymerase III subunit alpha
B: DNA polymerase III subunit epsilon,DNA polymerase III subunit alpha
C: DNA polymerase III subunit epsilon,DNA polymerase III subunit alpha
D: DNA polymerase III subunit epsilon,DNA polymerase III subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,6558
Polymers138,5134
Non-polymers1424
Water20,3211128
1
A: DNA polymerase III subunit epsilon,DNA polymerase III subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6642
Polymers34,6281
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA polymerase III subunit epsilon,DNA polymerase III subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6642
Polymers34,6281
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA polymerase III subunit epsilon,DNA polymerase III subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6642
Polymers34,6281
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DNA polymerase III subunit epsilon,DNA polymerase III subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6642
Polymers34,6281
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.470, 56.630, 138.010
Angle α, β, γ (deg.)90.00, 93.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGILEILEAA6 - 2646 - 264
21ARGARGILEILEBB6 - 2646 - 264
31ARGARGILEILECC6 - 2646 - 264
41ARGARGILEILEDD6 - 2646 - 264
12PROPROTHRTHRAA281 - 315281 - 315
22PROPROTHRTHRBB281 - 315281 - 315
32PROPROTHRTHRCC281 - 315281 - 315
42PROPROTHRTHRDD281 - 315281 - 315

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Components

#1: Protein
DNA polymerase III subunit epsilon,DNA polymerase III subunit alpha


Mass: 34628.246 Da / Num. of mol.: 4
Fragment: polIII epsilon C-terminal domain (UNP residues 209-243),polIII alpha PHP domain (UNP residues 1-270)
Mutation: L66P,L66P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dnaQ, mutD, b0215, JW0205, dnaE, polC, b0184, JW0179 / Plasmid: pETMCS1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 P lysS
References: UniProt: P03007, UniProt: P10443, DNA-directed DNA polymerase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1128 / 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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 0.2M MgCl2, 0.1M Tris, 16-18% PEG3350, 3mM TCEP, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.96858 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 1, 2010 / Details: beamline optics
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96858 Å / Relative weight: 1
ReflectionResolution: 1.7→23.24 Å / Num. all: 140494 / Num. obs: 140494 / % possible obs: 98.1 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 7 % / Biso Wilson estimate: 16.704 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 8.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 3.7 / Num. unique all: 20221 / % possible all: 97.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HNH

2hnh


Resolution: 1.7→23.04 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.667 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): -1 / ESU R: 0.13 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24556 7115 5.1 %RANDOM
Rwork0.21276 ---
all0.21442 140410 --
obs0.21442 140410 97.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.958 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20.36 Å2
2---0.96 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→23.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9595 0 4 1128 10727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02210119
X-RAY DIFFRACTIONr_angle_refined_deg1.1181.96813773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.16351332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05223.333480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.919151721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8711594
X-RAY DIFFRACTIONr_chiral_restr0.0770.21539
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217814
X-RAY DIFFRACTIONr_mcbond_it2.471.56326
X-RAY DIFFRACTIONr_mcangle_it3.546210176
X-RAY DIFFRACTIONr_scbond_it5.66333793
X-RAY DIFFRACTIONr_scangle_it8.2924.53552
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2148 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.175
Bloose positional0.195
Cloose positional0.195
Dloose positional0.185
Aloose thermal2.310
Bloose thermal2.1110
Cloose thermal1.9810
Dloose thermal1.810
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 498 -
Rwork0.23 9635 -
obs-10133 96.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.39180.6198-0.55741.1515-0.41391.5498-0.03140.12490.1031-0.10590.04840.08940.0032-0.0644-0.0170.01490.0003-0.01320.01420.00490.018840.939237.5351122.9029
21.3132-0.36040.22651.3089-0.3341.9112-0.0243-0.1175-0.10110.08430.04090.06620.0382-0.0364-0.01660.00750.00270.00370.01190.00650.015244.804954.759384.3518
31.48150.5222-0.57491.2054-0.42631.8562-0.0260.15470.0983-0.11530.05720.0925-0.0143-0.0882-0.03120.0137-0.0019-0.00950.01680.00960.0118-1.65820.4134122.2679
41.1918-0.27660.29881.1472-0.3591.6022-0.0097-0.0972-0.10330.07910.02790.0840.0303-0.035-0.01820.0143-00.00470.02310.00150.02052.549237.143883.9629
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 315
2X-RAY DIFFRACTION2B4 - 315
3X-RAY DIFFRACTION3C4 - 315
4X-RAY DIFFRACTION4D4 - 315

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