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- PDB-4gx9: Crystal structure of a DNA polymerase III alpha-epsilon chimera -

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Basic information

Entry
Database: PDB / ID: 4gx9
TitleCrystal structure of a DNA polymerase III alpha-epsilon chimera
ComponentsDNA polymerase III subunit epsilon,DNA polymerase III subunit alphaDNA polymerase III holoenzyme
KeywordsTRANSFERASE / DNA polymerase III / polIII epsilon / polIII alpha / DnaQ / DnaE
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-directed DNA polymerase ...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-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / metal ion binding / cytosol / cytoplasm
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: 2.15 Å
AuthorsLi, N. / Horan, N. / Xu, Z.-Q. / Jacques, D. / 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: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: diffrn_detector / entity ...diffrn_detector / entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _diffrn_detector.detector / _entity.pdbx_description ..._diffrn_detector.detector / _entity.pdbx_description / _entity.pdbx_ec / _entity.pdbx_fragment / _entity.pdbx_mutation
Revision 1.4Nov 8, 2023Group: Data collection / Database references / 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
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

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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


Theoretical massNumber of molelcules
Total (without water)142,7864
Polymers142,7864
Non-polymers00
Water4,990277
1
A: DNA polymerase III subunit epsilon,DNA polymerase III subunit alpha


Theoretical massNumber of molelcules
Total (without water)35,6971
Polymers35,6971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA polymerase III subunit epsilon,DNA polymerase III subunit alpha


Theoretical massNumber of molelcules
Total (without water)35,6971
Polymers35,6971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA polymerase III subunit epsilon,DNA polymerase III subunit alpha


Theoretical massNumber of molelcules
Total (without water)35,6971
Polymers35,6971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DNA polymerase III subunit epsilon,DNA polymerase III subunit alpha


Theoretical massNumber of molelcules
Total (without water)35,6971
Polymers35,6971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.017, 56.980, 135.073
Angle α, β, γ (deg.)90.00, 93.78, 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: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUTHRTHRAA5 - 3714 - 46
21LEULEUTHRTHRBB5 - 3714 - 46
31LEULEUTHRTHRCC5 - 3714 - 46
41LEULEUTHRTHRDD5 - 3714 - 46
12GLUGLUALAALAAA48 - 25757 - 266
22GLUGLUALAALABB48 - 25757 - 266
32GLUGLUALAALACC48 - 25757 - 266
42GLUGLUALAALADD48 - 25757 - 266
13TYRTYRTHRTHRAA279 - 315288 - 324
23TYRTYRTHRTHRBB279 - 315288 - 324
33TYRTYRTHRTHRCC279 - 315288 - 324
43TYRTYRTHRTHRDD279 - 315288 - 324

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Components

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


Mass: 35696.512 Da / Num. of mol.: 4
Fragment: polIII epsilon C-terminal domain (UNP residues 200-243),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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.23 Å3/Da / Density % sol: 44.9 %
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: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2012 / Details: beamline optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 67257 / Num. obs: 67257 / % possible obs: 97.2 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.41
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3361

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HNH

2hnh


Resolution: 2.15→35.28 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 16.553 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.327 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29079 3384 5 %RANDOM
Rwork0.2262 ---
all0.22948 67126 --
obs0.22948 67126 96.91 %-
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: 22.248 Å2
Baniso -1Baniso -2Baniso -3
1-2.45 Å20 Å21.09 Å2
2--0.63 Å2-0 Å2
3----2.93 Å2
Refinement stepCycle: LAST / Resolution: 2.15→35.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9700 0 0 277 9977
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02210008
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.96813593
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61351295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8523.433469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.169151676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2541588
X-RAY DIFFRACTIONr_chiral_restr0.1190.21525
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217692
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5041.56287
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.475210085
X-RAY DIFFRACTIONr_scbond_it5.55333721
X-RAY DIFFRACTIONr_scangle_it7.2724.53484
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2151 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.250.5
Bmedium positional0.230.5
Cmedium positional0.230.5
Dmedium positional0.250.5
Amedium thermal1.62
Bmedium thermal1.512
Cmedium thermal1.52
Dmedium thermal1.552
LS refinement shellResolution: 2.15→2.204 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 247 -
Rwork0.278 4593 -
obs--95.28 %
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)
11.8825-0.1515-0.40081.46750.1082.31260.0798-0.12260.11840.0924-0.0320.0148-0.0839-0.0062-0.04780.0246-0.0125-0.01930.0120.00380.0669-2.75064.5071-52.0334
22.33990.34070.19061.26510.31452.7640.01650.0876-0.0299-0.11810.0453-0.09940.01240.0616-0.06180.0266-0.00290.0050.05190.00240.0882-7.424922.9343-15.4472
32.40610.39460.12551.2070.4472.98980.04430.0953-0.0295-0.0497-0.0002-0.06210.0442-0.0411-0.04410.0144-0.0054-0.01430.03710.01130.056334.29527.4534-15.6573
42.4395-0.3629-0.53131.3510.21952.28660.0647-0.15930.09880.0849-0.0235-0.0473-0.10990.1006-0.04120.0331-0.0236-0.02150.0254-0.00270.075738.6351-10.5878-52.1532
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 315
2X-RAY DIFFRACTION2B-5 - 315
3X-RAY DIFFRACTION3C-5 - 315
4X-RAY DIFFRACTION4D4 - 315

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