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- PDB-1njg: Nucleotide-free form of an Isolated E. coli Clamp Loader Gamma Subunit -
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Open data
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Basic information
Entry | Database: PDB / ID: 1njg | ||||||
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Title | Nucleotide-free form of an Isolated E. coli Clamp Loader Gamma Subunit | ||||||
![]() | DNA polymerase III subunit gamma![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Podobnik, M. / Weitze, T.F. / O'Donnell, M. / Kuriyan, J. | ||||||
![]() | ![]() Title: Nucleotide-Induced Conformational Changes in an Isolated Escherichia coli DNA Polymerase III Clamp Loader Subunit Authors: Podobnik, M. / Weitze, T.F. / O'Donnell, M. / Kuriyan, 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 | ![]() | 107.1 KB | Display | ![]() |
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PDB format | ![]() | 82.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1njfC ![]() 1jr3S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | There are two copies (chains A and B) of the monomeric biological unit in the asymmetric unit. |
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Components
#1: Protein | ![]() Mass: 27499.430 Da / Num. of mol.: 2 / Fragment: N-terminal domains 1 and 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 41.71 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 3350, ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 27, 2002 |
Radiation | Monochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→100 Å / Num. obs: 21425 / Observed criterion σ(F): -1.5 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.8 / % possible all: 79 |
Reflection | *PLUS Lowest resolution: 100 Å / Num. obs: 23273 / % possible obs: 92.1 % / Num. measured all: 255606 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 79 % |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1JR3 Resolution: 2.2→56.85 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 366008.63 / Data cutoff high rms absF: 366008.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.1996 Å2 / ksol: 0.358159 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→56.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.28 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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