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- PDB-6dj8: Structure of DNA polymerase III subunit beta from Borrelia burgdo... -

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Basic information

Entry
Database: PDB / ID: 6dj8
TitleStructure of DNA polymerase III subunit beta from Borrelia burgdorferi in complex with a natural product
Components
  • Beta sliding clamp
  • Natural product peptide
KeywordsDNA BINDING PROTEIN / SSGCID / DNAN / DNA POLYMERASE III SUBUNIT BETA / GRISELMYCIN / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


DNA polymerase III complex / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase activity / DNA binding / cytoplasm
Similarity search - Function
DNA polymerase III, beta sliding clamp / DNA polymerase III, beta sliding clamp, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / DNA polymerase III beta subunit
Similarity search - Domain/homology
ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY / Beta sliding clamp
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
Streptomyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of DNA polymerase III subunit beta from Borrelia burgdorferi in complex with a natural product
Authors: Conrady, D.G. / Abendroth, J. / Higgins, T.W. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMay 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_validate_close_contact / struct_conn
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Structure summary
Category: pdbx_molecule_features / struct_site / struct_site_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta sliding clamp
B: Beta sliding clamp
C: Natural product peptide
D: Natural product peptide


Theoretical massNumber of molelcules
Total (without water)93,6844
Polymers93,6844
Non-polymers00
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-24 kcal/mol
Surface area33700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.380, 68.290, 86.320
Angle α, β, γ (deg.)90.000, 113.700, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta sliding clamp / Sliding clamp / Beta-clamp processivity factor / DNA polymerase III beta sliding clamp subunit / ...Sliding clamp / Beta-clamp processivity factor / DNA polymerase III beta sliding clamp subunit / DNA polymerase III subunit beta


Mass: 45726.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680) (bacteria)
Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: dnaN, BB_0438 / Plasmid: BobuA.17987.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P33761
#2: Protein/peptide Natural product peptide


Type: Peptide-like / Class: Inhibitor / Mass: 1115.449 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Streptomyces (bacteria) / References: ACE-MVA-MP8-NZC-LEU-MP8-LEU-MVA-PRO-MLU-GLY
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus Screen G4: 0.02M each Sodium formate, Ammonium acetate, Sodium citrate tribasic dihydrate, Sodium potassium tartrate tetrahydrate, Sodium oxamate: 0.1 M Imidazole/MES buffer pH 6.5, ...Details: Morpheus Screen G4: 0.02M each Sodium formate, Ammonium acetate, Sodium citrate tribasic dihydrate, Sodium potassium tartrate tetrahydrate, Sodium oxamate: 0.1 M Imidazole/MES buffer pH 6.5, 12.5% MPD, 12.5% PEG 1000, 12.5% PEG3350: mixed 0.4:0.4 with BobuA.17987.a.B1.PW38224 at 20mg/ml. Co-crystallized with 1mM Griselmycin: direct cryo: tray 292391G4: puck YYX8-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→42 Å / Num. obs: 56445 / % possible obs: 99.5 % / Redundancy: 4.118 % / Biso Wilson estimate: 47.42 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.046 / Χ2: 1.042 / Net I/σ(I): 19.17 / Num. measured all: 232442
Reflection shellResolution: 2.05→42 Å / Redundancy: 3.674 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.36 / Num. measured obs: 2436 / Num. possible: 693 / Num. unique obs: 663 / CC1/2: 0.998 / Rrim(I) all: 0.033 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIXDEV_3126refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→42 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 1992 3.53 %
Rwork0.202 --
obs0.203 56397 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.77 Å2 / Biso mean: 50.85 Å2 / Biso min: 26.51 Å2
Refinement stepCycle: final / Resolution: 2.05→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6158 0 0 207 6365
Biso mean---49.26 -
Num. residues----782
LS refinement shellResolution: 2.05→2.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.373 130 -
Rwork0.326 3740 -
all-3870 -
obs--96 %

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