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Open data
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Basic information
Entry | Database: PDB / ID: 8dkd | ||||||
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Title | Sliding clamp from M. thermoresistibile | ||||||
![]() | Beta sliding clamp | ||||||
![]() | DNA BINDING PROTEIN | ||||||
Function / homology | ![]() DNA polymerase III complex / DNA strand elongation involved in DNA replication / 3'-5' exonuclease activity / DNA-directed DNA polymerase activity / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kapur, M.K. / Gray, O.J. / Honzatko, R.H. / Nelson, S.N. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Interaction of sliding clamp with mycobacterial polymerases Authors: Kapur, M.K. / Gray, O.J. / Honzatko, R.H. / Nelson, S.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 184.5 KB | Display | ![]() |
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PDB format | ![]() | 119.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8dj6C ![]() 8dk9C ![]() 3p16S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41677.191 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316 Gene: KEK_10778 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.87 Å3/Da / Density % sol: 74.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 4 M ammonium acetate , 0.1 M bis-tris propane, 8% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Mar 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→44.79 Å / Num. obs: 12983 / % possible obs: 93 % / Redundancy: 8.2 % / Biso Wilson estimate: 116.7 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.03 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 3.2→3.2 Å / Rmerge(I) obs: 0.91 / Num. unique obs: 243 / CC1/2: 0.595 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3P16 Resolution: 3.2→19.97 Å / SU ML: 0.5149 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.1119 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 121.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→19.97 Å
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Refine LS restraints |
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LS refinement shell |
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