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- PDB-8dk9: Sliding-clamp-DinX peptide -

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Basic information

Entry
Database: PDB / ID: 8dk9
TitleSliding-clamp-DinX peptide
Components
  • Beta sliding clamp
  • DNA polymerase IV 1 peptide
KeywordsDNA BINDING PROTEIN
Function / homology
Function and homology information


DNA polymerase III complex / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA replication / DNA repair / magnesium ion binding / DNA binding / cytoplasm
Similarity search - Function
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 ...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 / DNA polymerase type-Y, HhH motif / IMS family HHH motif / DNA polymerase IV / : / : / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Roll / DNA/RNA polymerase superfamily / Alpha Beta
Similarity search - Domain/homology
ACETYL GROUP / AMINO GROUP / Beta sliding clamp / DNA polymerase IV 1
Similarity search - Component
Biological speciesMycolicibacterium thermoresistibile (bacteria)
Mycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 sliding clamp with mycobacterial polymerases
Authors: Kapur, M.K. / Gray, O.J. / Honzatko, R.H. / Nelson, S.N.
History
DepositionJul 5, 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

Downloads & links

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Assembly

Deposited unit
A: Beta sliding clamp
B: Beta sliding clamp
E: DNA polymerase IV 1 peptide
F: DNA polymerase IV 1 peptide
C: Beta sliding clamp
D: Beta sliding clamp
G: DNA polymerase IV 1 peptide
H: DNA polymerase IV 1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,14421
Polymers169,4848
Non-polymers66013
Water10,755597
1
A: Beta sliding clamp
B: Beta sliding clamp
E: DNA polymerase IV 1 peptide
F: DNA polymerase IV 1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,18612
Polymers84,7424
Non-polymers4448
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Beta sliding clamp
D: Beta sliding clamp
G: DNA polymerase IV 1 peptide
H: DNA polymerase IV 1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9589
Polymers84,7424
Non-polymers2165
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.072, 73.944, 81.343
Angle α, β, γ (deg.)82.769, 77.570, 87.746
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

#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 (bacteria)
Gene: dnaN, RMCT_1113 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A100XCQ4
#2: Protein/peptide
DNA polymerase IV 1 peptide / Pol IV 1


Mass: 693.745 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria) / References: UniProt: P63986, DNA-directed DNA polymerase

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Non-polymers , 5 types, 610 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ACE / ACETYL GROUP


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


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


Mass: 18.015 Da / Num. of mol.: 597 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Hepes ph 7.5, 0.1M lithium sulphate, 0.1 M NaCl, 20%PEG 3350 and 10% 1,6-Hexanediol

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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 PILATUS3 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: 2.5→47.35 Å / Num. obs: 52753 / % possible obs: 94.5 % / Redundancy: 1.7 % / Biso Wilson estimate: 48.89 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.068 / Net I/σ(I): 6.66
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.329 / Num. unique obs: 2313 / CC1/2: 0.634 / Rpim(I) all: 0.329

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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: 2.5→47.35 Å / SU ML: 0.373 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 27.9098
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2644 1999 3.79 %
Rwork0.2106 50754 -
obs0.2126 52753 95.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.11 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11676 0 37 597 12310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002311985
X-RAY DIFFRACTIONf_angle_d0.480816374
X-RAY DIFFRACTIONf_chiral_restr0.04131970
X-RAY DIFFRACTIONf_plane_restr0.00342161
X-RAY DIFFRACTIONf_dihedral_angle_d11.03384396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.30551340.26953494X-RAY DIFFRACTION90.7
2.56-2.630.35951320.27213578X-RAY DIFFRACTION93.08
2.63-2.710.34221620.25963554X-RAY DIFFRACTION93.74
2.71-2.80.30231270.2563567X-RAY DIFFRACTION94.67
2.8-2.90.31031530.25943651X-RAY DIFFRACTION95.12
2.9-3.010.32411420.26653610X-RAY DIFFRACTION95.06
3.01-3.150.31031380.25693645X-RAY DIFFRACTION95.31
3.15-3.320.33081480.24253660X-RAY DIFFRACTION95.92
3.32-3.520.31081410.22193652X-RAY DIFFRACTION95.35
3.52-3.80.24251500.21443636X-RAY DIFFRACTION96.14
3.8-4.180.24471420.18483711X-RAY DIFFRACTION96.25
4.18-4.780.24051410.16013675X-RAY DIFFRACTION96.41
4.78-6.020.22281400.18663655X-RAY DIFFRACTION96.3
6.02-47.350.20411490.18893666X-RAY DIFFRACTION96.24

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