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- PDB-5lew: DNA polymerase -

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Basic information

Entry
Database: PDB / ID: 5lew
TitleDNA polymerase
ComponentsDNA polymerase III subunit alphaDNA polymerase III holoenzyme
KeywordsTRANSFERASE / DNA Polymerase Multi-domain
Function / homology
Function and homology information


cell wall / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / plasma membrane / cytoplasm
Similarity search - Function
Bacterial DNA polymerase III alpha subunit, thumb 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 ...Bacterial DNA polymerase III alpha subunit, thumb 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 / Metal-dependent hydrolases / Arc Repressor Mutant, subunit A / TIM Barrel / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA polymerase III subunit alpha
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsBanos-Mateos, S. / Lang, U.F. / Maslen, S.L. / Skehel, J.M. / Lamers, M.H.
CitationJournal: Nat Commun / Year: 2017
Title: High-fidelity DNA replication in Mycobacterium tuberculosis relies on a trinuclear zinc center.
Authors: Banos-Mateos, S. / van Roon, A.M. / Lang, U.F. / Maslen, S.L. / Skehel, J.M. / Lamers, M.H.
History
DepositionJun 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase III subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,46414
Polymers102,1651
Non-polymers1,29913
Water1,45981
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-244 kcal/mol
Surface area39230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)256.044, 256.044, 187.350
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 102164.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: dnaE1, dnaE, Rv1547, MTCY48.18c
Production host: Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: P9WNT7, DNA-directed DNA polymerase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.2M lithium sulphate 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96864 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96864 Å / Relative weight: 1
ReflectionResolution: 2.8→49.09 Å / Num. obs: 57577 / % possible obs: 99.7 % / Redundancy: 3.4 % / CC1/2: 0.975 / Rmerge(I) obs: 0.207 / Rpim(I) all: 0.129 / Rrim(I) all: 0.244 / Net I/σ(I): 6.2 / Num. measured all: 197467 / Scaling rejects: 103
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.8-2.883.51.5011557744780.3150.9191.7651.299.7
12.2-49.093.10.05422507290.9860.0390.06717.197.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
XDSdata reduction
Aimless0.5.5data scaling
MOLREPphasing
Cootmodel building
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HNH

2hnh


Resolution: 2.8→143.11 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.909 / SU B: 11.841 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.298 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2306 2925 5.1 %RANDOM
Rwork0.1959 ---
obs0.1976 54650 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 202.86 Å2 / Biso mean: 49.364 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.12 Å20 Å2
2--0.24 Å20 Å2
3----0.77 Å2
Refinement stepCycle: final / Resolution: 2.8→143.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7109 0 63 81 7253
Biso mean--92.38 33.14 -
Num. residues----919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0197333
X-RAY DIFFRACTIONr_angle_refined_deg2.1391.9719941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4815921
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05223.254335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.279151209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.5621564
X-RAY DIFFRACTIONr_chiral_restr0.1380.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215605
X-RAY DIFFRACTIONr_mcbond_it4.6654.7253681
X-RAY DIFFRACTIONr_mcangle_it7.1247.0764600
X-RAY DIFFRACTIONr_scbond_it6.2835.0693651
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 230 -
Rwork0.366 4015 -
all-4245 -
obs--99.62 %

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