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- PDB-8dj6: Sliding-clamp-ImuB peptide -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8dj6
TitleSliding-clamp-ImuB peptide
Components
  • Beta sliding clamp
  • Imub-peptide
KeywordsDNA BINDING PROTEIN / Sliding clamp in complex with ImuB peptide
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, N-terminal / DNA polymerase III, beta sliding clamp, C-terminal / DNA polymerase III, beta sliding clamp, central / DNA polymerase III beta subunit / DNA polymerase III, beta sliding clamp / DNA polymerase III beta subunit, N-terminal domain / DNA polymerase III beta subunit, central domain / DNA polymerase III beta subunit, C-terminal domain / :
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / Beta sliding clamp
Similarity search - Component
Biological speciesMycolicibacterium thermoresistibile ATCC 19527 (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
DepositionJun 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta sliding clamp
C: Beta sliding clamp
B: Beta sliding clamp
D: Beta sliding clamp
E: Imub-peptide
F: Imub-peptide
G: Imub-peptide
H: Imub-peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,03816
Polymers169,6568
Non-polymers3818
Water6,684371
1
A: Beta sliding clamp
B: Beta sliding clamp
E: Imub-peptide
F: Imub-peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,11710
Polymers84,8284
Non-polymers2896
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Beta sliding clamp
D: Beta sliding clamp
G: Imub-peptide
H: Imub-peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9206
Polymers84,8284
Non-polymers922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)214.110, 124.832, 117.262
Angle α, β, γ (deg.)90.000, 113.749, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,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 / Production host: Escherichia coli (E. coli) / References: UniProt: G7CIP4
#2: Protein/peptide
Imub-peptide


Mass: 736.882 Da / Num. of mol.: 4 / Source method: obtained synthetically
Source: (synth.) Mycolicibacterium thermoresistibile ATCC 19527 (bacteria)
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 4.31 Å3/Da / Density % sol: 71.45 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bis -Tris pH6.3, 60% Tascimate pH7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→46.75 Å / Num. obs: 94524 / % possible obs: 96.4 % / Redundancy: 3 % / Biso Wilson estimate: 54.86 Å2 / CC1/2: 0.963 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.082 / Net I/σ(I): 10.3
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.988 / Mean I/σ(I) obs: 0.88 / Num. unique obs: 4590 / CC1/2: 0.4 / Rpim(I) all: 0.671

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TR7

4tr7


Resolution: 2.5→46.75 Å / SU ML: 0.3461 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.0738
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2261 1998 2.12 %
Rwork0.1996 92386 -
obs0.2002 94384 96.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11700 0 41 371 12112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002411992
X-RAY DIFFRACTIONf_angle_d0.502416373
X-RAY DIFFRACTIONf_chiral_restr0.04151970
X-RAY DIFFRACTIONf_plane_restr0.00352159
X-RAY DIFFRACTIONf_dihedral_angle_d10.30984383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.34031270.30325889X-RAY DIFFRACTION86.49
2.56-2.630.28541410.28756473X-RAY DIFFRACTION95.08
2.63-2.710.33681420.27776560X-RAY DIFFRACTION95.66
2.71-2.790.29131400.27556548X-RAY DIFFRACTION95.84
2.79-2.890.3511420.28446538X-RAY DIFFRACTION96.31
2.89-3.010.26191440.2576615X-RAY DIFFRACTION96.52
3.01-3.150.24591410.2316558X-RAY DIFFRACTION96.46
3.15-3.310.26521430.22966625X-RAY DIFFRACTION97.07
3.31-3.520.2691440.21336676X-RAY DIFFRACTION97.55
3.52-3.790.2311460.1816735X-RAY DIFFRACTION97.98
3.79-4.170.20151460.16726751X-RAY DIFFRACTION98.44
4.17-4.770.16391460.13646779X-RAY DIFFRACTION98.59
4.77-6.010.18861480.16976800X-RAY DIFFRACTION98.79
6.01-46.750.19721480.26839X-RAY DIFFRACTION97.9

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