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Yorodumi- PDB-1njf: Nucleotide bound form of an isolated E. coli clamp loader gamma s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1njf | ||||||
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Title | Nucleotide bound form of an isolated E. coli clamp loader gamma subunit | ||||||
Components | DNA polymerase III subunit gamma | ||||||
Keywords | TRANSFERASE / protein-nucleotide complex / 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 / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 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 | 1njf.cif.gz | 202 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1njf.ent.gz | 161.5 KB | Display | PDB format |
PDBx/mmJSON format | 1njf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1njf_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1njf_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1njf_validation.xml.gz | 42.5 KB | Display | |
Data in CIF | 1njf_validation.cif.gz | 57.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/1njf ftp://data.pdbj.org/pub/pdb/validation_reports/nj/1njf | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Details | There are four copies (chains A, B, C and D) of the monomeric biological unit in the asymmetric unit. |
-Components
#1: Protein | Mass: 27499.430 Da / Num. of mol.: 4 / 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 | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-ADP / | #5: 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: 2.24 Å3/Da / Density % sol: 44.67 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 2.8 Details: PEG 10000, KNO3, 1,4-Butanediol, pH 2.8, 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: 5.0.2 / Wavelength: 1.24345 , 1.28201, 1.28243 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 31, 2002 | ||||||||||||
Radiation | Monochromator: Double-crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→100 Å / Num. obs: 81300 / Observed criterion σ(F): -1.5 / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 34.5 | ||||||||||||
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 8.7 / % possible all: 84.4 | ||||||||||||
Reflection | *PLUS Lowest resolution: 100 Å / Num. obs: 45447 / % possible obs: 96.5 % / Num. measured all: 1061344 | ||||||||||||
Reflection shell | *PLUS % possible obs: 84.4 % / Rmerge(I) obs: 0.24 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→82.84 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 263324.48 / Data cutoff high rms absF: 263324.48 / 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: 31.7841 Å2 / ksol: 0.354096 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→82.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.211 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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