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Yorodumi- PDB-1njg: Nucleotide-free form of an Isolated E. coli Clamp Loader Gamma Subunit -
+Open data
-Basic information
Entry | Database: PDB / ID: 1njg | ||||||
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Title | Nucleotide-free form of an Isolated E. coli Clamp Loader Gamma Subunit | ||||||
Components | DNA polymerase III subunit gammaDNA polymerase III holoenzyme | ||||||
Keywords | TRANSFERASE / Rossman-like fold / AAA+ ATPase domains / sensor 1 / sensor 2 | ||||||
Function / homology | Function and homology information DNA polymerase III, clamp loader complex / DNA polymerase III complex / replisome / DNA polymerase processivity factor activity / ribonucleoside triphosphate phosphatase activity / DNA-templated DNA replication / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / ATP hydrolysis activity ...DNA polymerase III, clamp loader complex / DNA polymerase III complex / replisome / DNA polymerase processivity factor activity / ribonucleoside triphosphate phosphatase activity / DNA-templated DNA replication / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Podobnik, M. / Weitze, T.F. / O'Donnell, M. / Kuriyan, J. | ||||||
Citation | Journal: Structure / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1njg.cif.gz | 107.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1njg.ent.gz | 82.5 KB | Display | PDB format |
PDBx/mmJSON format | 1njg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/1njg ftp://data.pdbj.org/pub/pdb/validation_reports/nj/1njg | HTTPS FTP |
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-Related structure data
Related structure data | 1njfC 1jr3S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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. |
-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.) Escherichia coli (E. coli) / Gene: DnaX / Plasmid: pGEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06710, DNA-directed DNA polymerase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
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: 1 Å / Relative weight: 1 |
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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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: 0.265 / Rfactor Rwork: 0.235 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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