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Yorodumi- PDB-4n98: E. coli sliding clamp in complex with 4'-fluorobiphenyl-4-carboxy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4n98 | ||||||
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Title | E. coli sliding clamp in complex with 4'-fluorobiphenyl-4-carboxylic acid | ||||||
Components | DNA polymerase III subunit betaDNA polymerase III holoenzyme | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / PolIII beta / sliding clamp / DnaN / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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: 1.7 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 | 4n98.cif.gz | 163 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n98.ent.gz | 126.7 KB | Display | PDB format |
PDBx/mmJSON format | 4n98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/4n98 ftp://data.pdbj.org/pub/pdb/validation_reports/n9/4n98 | HTTPS FTP |
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-Related structure data
Related structure data | 4n94C 4n95C 4n96C 4n97C 4n99C 4n9aC 1mmiS 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
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 5 types, 501 molecules
#2: Chemical | ChemComp-4FC / | ||||||
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#3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.65 % |
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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 | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.7→73.989 Å / Num. all: 86092 / Num. obs: 86092 / % possible obs: 99.9 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 7 % / Rsym value: 0.097 / Net I/σ(I): 9.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 1MMI Resolution: 1.7→30.17 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.885 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 3.135 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.141 / 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: 62.27 Å2 / Biso mean: 24.3463 Å2 / Biso min: 12.06 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→30.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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