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- PDB-4jom: Structure of E. coli Pol III 3mPHP mutant -

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Basic information

Entry
Database: PDB / ID: 4jom
TitleStructure of E. coli Pol III 3mPHP mutant
ComponentsDNA polymerase III subunit alphaDNA polymerase III holoenzyme
KeywordsTRANSFERASE / DNA polymerase / DNA binding / dNTP binding
Function / homology
Function and homology information


DNA polymerase III, core complex / DNA polymerase III complex / lagging strand elongation / replisome / leading strand elongation / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / cytosol / cytoplasm
Similarity search - Function
Bacterial DNA polymerase III alpha subunit, thumb domain / : / : / DNA polymerase III subunit alpha, C-terminal 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 ...Bacterial DNA polymerase III alpha subunit, thumb domain / : / : / DNA polymerase III subunit alpha, C-terminal 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 / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Metal-dependent hydrolases / Arc Repressor Mutant, subunit A / Nucleic acid-binding, OB-fold / TIM Barrel / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / DNA polymerase III subunit alpha
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBarros, T. / Guenther, J. / Kelch, B. / Anaya, J. / Prabhakar, A. / O'Donnell, M. / Kuriyan, J. / Lamers, M.H.
CitationJournal: Bmc Struct.Biol. / Year: 2013
Title: A structural role for the PHP domain in E. coli DNA polymerase III.
Authors: Barros, T. / Guenther, J. / Kelch, B. / Anaya, J. / Prabhakar, A. / O Donnell, M. / Kuriyan, J. / Lamers, M.H.
History
DepositionMar 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_ref_seq_dif / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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 alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0977
Polymers102,5891
Non-polymers5086
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.429, 98.944, 139.879
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 102589.195 Da / Num. of mol.: 1 / Fragment: 3mPHP (UNP residues 1-917) / Mutation: yes
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dnaE, polC, b0184, JW0179 / Production host: Escherichia coli (E. coli) / References: UniProt: P10443, DNA-directed DNA polymerase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 10-15 mg/mL protein, 15-20% PEG3350, 0.2-0.4 M sodium phosphate monobasic, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2008
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.9→46.945 Å / Num. all: 26380 / Num. obs: 26274 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.9→3.07 Å / % possible all: 97.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HNH

2hnh


Resolution: 2.9→46.945 Å / SU ML: 0.32 / σ(F): 1.35 / Phase error: 25.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2452 1342 5.16 %
Rwork0.1939 --
obs0.1966 26012 99.98 %
all-26380 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→46.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7139 0 23 19 7181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037325
X-RAY DIFFRACTIONf_angle_d0.7339906
X-RAY DIFFRACTIONf_dihedral_angle_d14.6552745
X-RAY DIFFRACTIONf_chiral_restr0.0421073
X-RAY DIFFRACTIONf_plane_restr0.0031303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.00370.31541420.2782415X-RAY DIFFRACTION100
3.0037-3.1240.34291130.2672436X-RAY DIFFRACTION100
3.124-3.26610.30321350.25762426X-RAY DIFFRACTION100
3.2661-3.43830.31981470.22112425X-RAY DIFFRACTION100
3.4383-3.65360.22181190.20282453X-RAY DIFFRACTION100
3.6536-3.93560.23931400.18552439X-RAY DIFFRACTION100
3.9356-4.33140.20841220.15872476X-RAY DIFFRACTION100
4.3314-4.95750.1881370.15552480X-RAY DIFFRACTION100
4.9575-6.24360.22911550.18922480X-RAY DIFFRACTION100
6.2436-46.9510.2481320.18482640X-RAY DIFFRACTION100
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)
11.96870.10850.42530.8862-0.32450.8210.1331-0.0624-0.1223-0.06370.00980.17040.1297-0.0152-0.1140.30660.01420.00240.35990.04710.314.370416.11537.7471
21.3584-0.13230.35271.1365-0.76041.1256-0.0269-0.5214-0.08760.17330.33130.1732-0.2324-0.2383-0.24160.70240.1397-0.01980.66730.17780.492620.4224-6.891931.6119
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 593 )
2X-RAY DIFFRACTION2chain 'A' and (resid 594 through 911 )

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