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- PDB-4k3k: E. Coli sliding clamp in complex with (S)-2-(4-methylpentanamido)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4k3k | ||||||
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Title | E. Coli sliding clamp in complex with (S)-2-(4-methylpentanamido)-3-phenylpropanoic acid | ||||||
![]() | DNA polymerase III subunit beta | ||||||
![]() | TRANSFERASE / PolIII beta / sliding clamp / DnaN | ||||||
Function / homology | ![]() Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / error-prone translesion synthesis / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity ...Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / error-prone translesion synthesis / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase activity / DNA damage response / protein homodimerization activity / DNA binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Yin, Z. / Oakley, A.J. | ||||||
![]() | ![]() Title: Structural and Thermodynamic Dissection of Linear Motif Recognition by the E. coli Sliding Clamp Authors: Yin, Z. / Kelso, M.J. / Beck, J.L. / Oakley, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 168.3 KB | Display | ![]() |
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PDB format | ![]() | 130.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 732.2 KB | Display | ![]() |
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Full document | ![]() | 737.8 KB | Display | |
Data in XML | ![]() | 33.5 KB | Display | |
Data in CIF | ![]() | 50.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4k3lC ![]() 4k3mC ![]() 4k3oC ![]() 4k3pC ![]() 4k3qC ![]() 4k3rC ![]() 4k3sC ![]() 1mmiS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 40630.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 631 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SFK.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/SFK.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-PG4 / #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-SFK / | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.14 % / Mosaicity: 0.573 ° |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100mM MES, 100-150mM CaCl2, 25-30%(v/v) PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 22, 2012 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→50 Å / Num. all: 56309 / Num. obs: 56309 / % possible obs: 93.2 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.029 / Χ2: 0.973 / Net I/σ(I): 28.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1MMI Resolution: 1.85→34.95 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 3.312 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 51.87 Å2 / Biso mean: 18.9354 Å2 / Biso min: 6.93 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→34.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.854→1.902 Å / Total num. of bins used: 20
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