+Open data
-Basic information
Entry | Database: PDB / ID: 1xxi | ||||||
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Title | ADP Bound E. coli Clamp Loader Complex | ||||||
Components |
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Keywords | TRANSFERASE / AAA+ ATPase / clamp loader / DNA polymerase III / DNA replication | ||||||
Function / homology | Function and homology information DNA polymerase III, clamp loader complex / DNA polymerase III complex / replisome / DNA polymerase processivity factor activity / 3'-5' exonuclease activity / ribonucleoside triphosphate phosphatase activity / DNA-templated DNA replication / DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity ...DNA polymerase III, clamp loader complex / DNA polymerase III complex / replisome / DNA polymerase processivity factor activity / 3'-5' exonuclease 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: 4.1 Å | ||||||
Authors | Kazmirski, S.L. / Podobnik, M. / Weitze, T.F. / O'Donnell, M. / Kuriyan, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Structural analysis of the inactive state of the Escherichia coli DNA polymerase clamp-loader complex Authors: Kazmirski, S.L. / 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 | 1xxi.cif.gz | 590.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xxi.ent.gz | 473.1 KB | Display | PDB format |
PDBx/mmJSON format | 1xxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/1xxi ftp://data.pdbj.org/pub/pdb/validation_reports/xx/1xxi | HTTPS FTP |
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-Related structure data
Related structure data | 1xxhC 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 2 clamp loader complexes in the asymmetric unit. One consists of chains A-E and the second consists of chains F-J |
-Components
-DNA polymerase III, delta ... , 2 types, 4 molecules AFEJ
#1: Protein | Mass: 38745.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: holA / Production host: Escherichia coli (E. coli) / References: UniProt: P28630, DNA-directed DNA polymerase #3: Protein | Mass: 36980.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: holB / Production host: Escherichia coli (E. coli) / References: UniProt: P28631, DNA-directed DNA polymerase |
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-Protein , 1 types, 6 molecules BCDGHI
#2: Protein | Mass: 40900.172 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaX, dnaZ, dnaZX / Production host: Escherichia coli (E. coli) / References: UniProt: P06710, DNA-directed DNA polymerase |
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-Non-polymers , 3 types, 12 molecules
#4: Chemical | ChemComp-ZN / #5: Chemical | #6: Chemical | ChemComp-PO4 / | |
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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: 3.62 Å3/Da / Density % sol: 65.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.95 Details: PEG 3350, Sodium Phosphate, Anapoe X-405, pH 7.95, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 18, 2003 |
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: 4.1→100 Å / Num. obs: 45400 / % possible obs: 94 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 4.1→4.2 Å / % possible all: 83.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1JR3 Resolution: 4.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 4.1→20 Å
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