+Open data
-Basic information
Entry | Database: PDB / ID: 4n97 | ||||||
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Title | E. coli sliding clamp in complex with 5-nitroindole | ||||||
Components | DNA polymerase III subunit beta | ||||||
Keywords | TRANSFERASE / sliding clamp / DnaN | ||||||
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: 1.97 Å | ||||||
Authors | Yin, Z. / Oakley, A.J. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Discovery of lead compounds targeting the bacterial sliding clamp using a fragment-based approach. Authors: Yin, Z. / Whittell, L.R. / Wang, Y. / Jergic, S. / Liu, M. / Harry, E.J. / Dixon, N.E. / Beck, J.L. / Kelso, M.J. / Oakley, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n97.cif.gz | 168.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n97.ent.gz | 131 KB | Display | PDB format |
PDBx/mmJSON format | 4n97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4n97_validation.pdf.gz | 456.1 KB | Display | wwPDB validaton report |
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Full document | 4n97_full_validation.pdf.gz | 465.2 KB | Display | |
Data in XML | 4n97_validation.xml.gz | 35.1 KB | Display | |
Data in CIF | 4n97_validation.cif.gz | 52.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/4n97 ftp://data.pdbj.org/pub/pdb/validation_reports/n9/4n97 | HTTPS FTP |
-Related structure data
Related structure data | 4n94C 4n95C 4n96C 4n98C 4n99C 4n9aC 4k3sS 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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Unit cell |
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-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) / Strain: K12 / Gene: b3701, dnaN, JW3678 / Plasmid: pND261 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A988, DNA-directed DNA polymerase #2: Chemical | ChemComp-2HU / | #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-CA / | #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: 2.26 Å3/Da / Density % sol: 45.52 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 100mM MES, 100-150mM CaCl2, 25-30%(v/v) PEG400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 18, 2011 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.97→69.554 Å / Num. all: 42650 / Num. obs: 42650 / % possible obs: 84.8 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 3.6 % / Rsym value: 0.056 / Net I/σ(I): 12.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4K3S Resolution: 1.97→28.9 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.84 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 7.416 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.322 / ESU R Free: 0.258 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.66 Å2 / Biso mean: 21.6919 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→28.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.021 Å / Total num. of bins used: 20
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