+Open data
-Basic information
Entry | Database: PDB / ID: 1mmi | ||||||
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Title | E. COLI DNA POLYMERASE BETA SUBUNIT | ||||||
Components | DNA polymerase III, beta chain | ||||||
Keywords | TRANSFERASE / DNA POLYMERASE BETA SUBUNIT / E. COLI / DNA REPLICATION / SLIDING CLAMP / PROCESSIVITY FACTOR | ||||||
Function / homology | Function and homology information Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / error-prone translesion synthesis / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity ...Hda-beta clamp complex / bacterial-type DNA replication / replication inhibiting complex / DNA polymerase III complex / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / error-prone translesion synthesis / negative regulation of DNA-templated DNA replication initiation / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase activity / DNA damage response / protein homodimerization activity / DNA binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.848 Å | ||||||
Authors | Oakley, A.J. / Prosselkov, P. / Wijffels, G. / Beck, J.L. / Wilce, M.C.J. / Dixon, N.E. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Flexibility revealed by the 1.85 A crystal structure of the beta sliding-clamp subunit of Escherichia coli DNA polymerase III. Authors: Oakley, A.J. / Prosselkov, P. / Wijffels, G. / Beck, J.L. / Wilce, M.C. / Dixon, N.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mmi.cif.gz | 169 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mmi.ent.gz | 135.9 KB | Display | PDB format |
PDBx/mmJSON format | 1mmi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mmi_validation.pdf.gz | 441.8 KB | Display | wwPDB validaton report |
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Full document | 1mmi_full_validation.pdf.gz | 470 KB | Display | |
Data in XML | 1mmi_validation.xml.gz | 38.5 KB | Display | |
Data in CIF | 1mmi_validation.cif.gz | 56.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mm/1mmi ftp://data.pdbj.org/pub/pdb/validation_reports/mm/1mmi | HTTPS FTP |
-Related structure data
Related structure data | 2polS 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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Unit cell |
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Details | Asymmetric unit contains physiologically relevant dimer |
-Components
#1: Protein | Mass: 40630.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dnaN / Plasmid: pND261 / Production host: Escherichia coli (E. coli) / Strain (production host): AN1459 / References: UniProt: P0A988, DNA-directed DNA polymerase #2: 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: 2.42 Å3/Da / Density % sol: 49.13 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM Na/H MES, 50 to 60 mM CaCl2, 30% v/v PEG 400, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 294 K / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
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: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 23, 2001 |
Radiation | Monochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 62043 / Num. obs: 62043 / Observed criterion σ(I): -2 / Redundancy: 1.92 % / Rmerge(I) obs: 0.056 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 1.84 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 1.75 / % possible all: 91.7 |
Reflection | *PLUS Lowest resolution: 50 Å / % possible obs: 93.4 % |
Reflection shell | *PLUS % possible obs: 91.7 % / Num. unique obs: 6056 / Mean I/σ(I) obs: 1.76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2POL Resolution: 1.848→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.938 / SU ML: 0.116 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.719 Å2
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Refinement step | Cycle: LAST / Resolution: 1.848→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.848→1.896 Å / Total num. of bins used: 20 /
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Software | *PLUS Version: 5.1.19 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.85 Å / Lowest resolution: 50 Å / Rfactor Rfree: 0.2446 / Rfactor Rwork: 0.1884 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.85 Å / Lowest resolution: 1.9 Å |