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- PDB-2p1j: Crystal structure of a polC-type DNA polymerase III exonuclease d... -

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Basic information

Entry
Database: PDB / ID: 2p1j
TitleCrystal structure of a polC-type DNA polymerase III exonuclease domain from Thermotoga maritima
ComponentsDNA polymerase III polC-type
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / EXONUCLEASE / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #140 / DNA polymerase III, alpha subunit, Gram-positive type / DNA polymerase III epsilon subunit, exonuclease domain / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #140 / DNA polymerase III, alpha subunit, Gram-positive type / DNA polymerase III epsilon subunit, exonuclease domain / 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 / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H-like superfamily/Ribonuclease H / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA polymerase III PolC-type
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsBonanno, J.B. / Rutter, M. / Bain, K.T. / Izuka, M. / Sridhar, V. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a polC-type DNA polymerase III exonuclease domain from Thermotoga maritima
Authors: Bonanno, J.B. / Rutter, M. / Bain, K.T. / Izuka, M. / Sridhar, V. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMar 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2012Group: Structure summary
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.6Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.7Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase III polC-type
B: DNA polymerase III polC-type


Theoretical massNumber of molelcules
Total (without water)42,8132
Polymers42,8132
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-49 kcal/mol
Surface area17960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.703, 124.939, 143.062
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-6-

HOH

Detailsdomain swapped dimer

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Components

#1: Protein DNA polymerase III polC-type / PolIII


Mass: 21406.461 Da / Num. of mol.: 2 / Fragment: exonuclease domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Species: Thermotoga maritima / Strain: MSB8, DSM 3109, JCM 10099 / Gene: polC, TM_0576 / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZHF6, DNA-directed DNA polymerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8.6
Details: 100mM Tris-HCl pH 8.6, 20% Glycerol, 14% PEG 10000, 150mM Sodium chloride, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 24, 2007
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.5→24.05 Å / Num. all: 17030 / Num. obs: 17030 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 69.7 Å2 / Rmerge(I) obs: 0.106 / Rsym value: 0.106 / Net I/σ(I): 14.9
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.816 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2323 / Rsym value: 0.816 / % possible all: 91.5

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.886 / SU B: 11.231 / SU ML: 0.259 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.447 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.298 848 5 %RANDOM
Rwork0.229 ---
obs0.232 16961 96.02 %-
all-16961 --
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: 64.804 Å2
Baniso -1Baniso -2Baniso -3
1-3.53 Å20 Å20 Å2
2--1.75 Å20 Å2
3----5.28 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2723 0 0 86 2809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222776
X-RAY DIFFRACTIONr_angle_refined_deg1.9581.9673746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2735333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.84723.561132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.85115519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6691522
X-RAY DIFFRACTIONr_chiral_restr0.1440.2426
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022054
X-RAY DIFFRACTIONr_nbd_refined0.2670.21322
X-RAY DIFFRACTIONr_nbtor_refined0.320.21852
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2112
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.213
X-RAY DIFFRACTIONr_mcbond_it1.0591.51719
X-RAY DIFFRACTIONr_mcangle_it1.80822701
X-RAY DIFFRACTIONr_scbond_it2.30631197
X-RAY DIFFRACTIONr_scangle_it3.6214.51045
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 70 -
Rwork0.279 1078 -
obs-1148 90.39 %

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