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- PDB-8djq: Sliding-clamp-DnaE1 peptide -

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Basic information

Entry
Database: PDB / ID: 8djq
TitleSliding-clamp-DnaE1 peptide
Components
  • Beta sliding clamp
  • DNA polymerase III subunit alpha peptide
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


DNA polymerase III complex / DNA strand elongation involved in DNA replication / 3'-5' exonuclease activity / DNA-directed DNA polymerase / nucleic acid binding / DNA-directed DNA polymerase activity / DNA replication / DNA binding / cytoplasm
Similarity search - Function
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 ...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 / DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / 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 / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / : / Roll / Alpha Beta
Similarity search - Domain/homology
ACETYL GROUP / AMINO GROUP / Beta sliding clamp / DNA polymerase III subunit alpha
Similarity search - Component
Biological speciesMycolicibacterium thermoresistibile ATCC 19527 (bacteria)
Mycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKapur, M.K. / Gray, O.J. / Honzatko, R.H. / Nelson, S.N.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: To Be Published
Title: Interaction of the sliding clamp with mycobacterial polymerases
Authors: Kapur, M.K. / Gray, O.J. / Honzatko, R.H. / Nelson, S.N.
History
DepositionJul 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
E: DNA polymerase III subunit alpha peptide
F: DNA polymerase III subunit alpha peptide
C: Beta sliding clamp
D: Beta sliding clamp
G: DNA polymerase III subunit alpha peptide
H: DNA polymerase III subunit alpha peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,85216
Polymers169,6128
Non-polymers2408
Water9,080504
1
C: Beta sliding clamp
D: Beta sliding clamp
G: DNA polymerase III subunit alpha peptide
H: DNA polymerase III subunit alpha peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9268
Polymers84,8064
Non-polymers1204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta sliding clamp
B: Beta sliding clamp
E: DNA polymerase III subunit alpha peptide
F: DNA polymerase III subunit alpha peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9268
Polymers84,8064
Non-polymers1204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-25 kcal/mol
Surface area35430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.810, 148.252, 81.952
Angle α, β, γ (deg.)90.000, 92.183, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Beta sliding clamp


Mass: 41677.191 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium thermoresistibile ATCC 19527 (bacteria)
Strain: ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316
Gene: KEK_10778 / Plasmid: pSUMO / Production host: Escherichia coli (E. coli) / References: UniProt: G7CIP4
#2: Protein/peptide
DNA polymerase III subunit alpha peptide


Mass: 725.789 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria) / References: UniProt: P63978, DNA-directed DNA polymerase
#3: Chemical
ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NH2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5M Ammonium sulphate, 0.1 M sodium acetate tribasic pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→48.062 Å / Num. obs: 38932 / % possible obs: 99.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 60.4 Å2 / CC1/2: 0.967 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.098 / Net I/σ(I): 4.75
Reflection shellResolution: 2.8→2.85 Å / Num. unique obs: 1673 / CC1/2: 0.967

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8DJ6

8dj6


Resolution: 2.8→19.87 Å / SU ML: 0.5943 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.0642
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2849 1351 3.47 %
Rwork0.226 37579 -
obs0.2281 38930 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.2 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11656 0 16 504 12176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211973
X-RAY DIFFRACTIONf_angle_d0.478716351
X-RAY DIFFRACTIONf_chiral_restr0.04091976
X-RAY DIFFRACTIONf_plane_restr0.00322154
X-RAY DIFFRACTIONf_dihedral_angle_d10.5294392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90.46571350.36613760X-RAY DIFFRACTION99.39
2.9-3.020.37751360.3133726X-RAY DIFFRACTION99.66
3.02-3.150.37481360.29913764X-RAY DIFFRACTION99.72
3.15-3.320.36541300.26773736X-RAY DIFFRACTION99.79
3.32-3.520.32151350.25063772X-RAY DIFFRACTION99.82
3.52-3.790.38521330.24523709X-RAY DIFFRACTION98.72
3.8-4.170.24811400.20313782X-RAY DIFFRACTION99.82
4.17-4.770.20491340.17063756X-RAY DIFFRACTION99.54
4.77-5.980.22911340.19583778X-RAY DIFFRACTION99.69
5.99-19.870.24241380.20523796X-RAY DIFFRACTION99.17

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