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- PDB-4pnv: E. coli sliding clamp apo-crystal in P21 space group with larger ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4pnv | ||||||
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Title | E. coli sliding clamp apo-crystal in P21 space group with larger cell dimensions | ||||||
![]() | DNA polymerase III subunit beta | ||||||
![]() | TRANSFERASE / PolIII beta / sliding clamp / DnaN | ||||||
Function / homology | DNA Polymerase III; Chain A, domain 2 / DNA Polymerase III, subunit A, domain 2 / Roll / Alpha Beta / DI(HYDROXYETHYL)ETHER / : ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Yin, Z. / Oakley, A.J. | ||||||
![]() | ![]() Title: Bacterial Sliding Clamp Inhibitors that Mimic the Sequential Binding Mechanism of Endogenous Linear Motifs. Authors: Yin, Z. / Whittell, L.R. / Wang, Y. / Jergic, S. / Ma, C. / Lewis, P.J. / Dixon, N.E. / Beck, J.L. / Kelso, M.J. / 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 | ![]() | 178.2 KB | Display | ![]() |
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PDB format | ![]() | 139.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 405 KB | Display | ![]() |
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Full document | ![]() | 408.5 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 29.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ovfC ![]() 4ovgC ![]() 4ovhC ![]() 4pnuC ![]() 4pnwC ![]() 1mmiS C: citing same article ( S: Starting model for refinement |
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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
#1: Protein | Mass: 40630.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-CL / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.74 % |
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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: Nov 10, 2013 / Details: mirrros | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.86→30 Å / Num. all: 71719 / Num. obs: 71208 / % possible obs: 99.3 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.028 / Χ2: 0.87 / Net I/σ(I): 19.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1MMI Resolution: 1.86→27.55 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.18 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / 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: 67.41 Å2 / Biso mean: 20.921 Å2 / Biso min: 9.61 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→27.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.861→1.909 Å / Total num. of bins used: 20
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