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Yorodumi- PDB-5ah4: The sliding clamp of Mycobacterium smegmatis in complex with a na... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ah4 | ||||||||||||
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Title | The sliding clamp of Mycobacterium smegmatis in complex with a natural product. | ||||||||||||
Components |
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Keywords | TRANSFERASE/ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC COMPLEX / DNAN / DNA POLYMERASE / TUBERCULOSIS | ||||||||||||
Function / homology | Function and homology information DNA polymerase III complex / 3'-5' exonuclease activity / DNA replication / DNA-directed DNA polymerase activity / response to antibiotic / DNA binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | MYCOBACTERIUM SMEGMATIS (bacteria) STREPTOMYCES CAELICUS (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.313 Å | ||||||||||||
Authors | Lukat, P. / Kling, A. / Heinz, D.W. / Mueller, R. | ||||||||||||
Citation | Journal: Science / Year: 2015 Title: Antibiotics. Targeting Dnan for Tuberculosis Therapy Using Novel Griselimycins. Authors: Kling, A. / Lukat, P. / Almeida, D.V. / Bauer, A. / Fontaine, E. / Sordello, S. / Zaburannyi, N. / Herrmann, J. / Wenzel, S.C. / Konig, C. / Ammerman, N.C. / Barrio, M.B. / Borchers, K. / ...Authors: Kling, A. / Lukat, P. / Almeida, D.V. / Bauer, A. / Fontaine, E. / Sordello, S. / Zaburannyi, N. / Herrmann, J. / Wenzel, S.C. / Konig, C. / Ammerman, N.C. / Barrio, M.B. / Borchers, K. / Bordon-Pallier, F. / Bronstrup, M. / Courtemanche, G. / Gerlitz, M. / Geslin, M. / Hammann, P. / Heinz, D.W. / Hoffmann, H. / Klieber, S. / Kohlmann, M. / Kurz, M. / Lair, C. / Matter, H. / Nuermberger, E. / Tyagi, S. / Fraisse, L. / Grosset, J.H. / Lagrange, S. / Muller, R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ah4.cif.gz | 307.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ah4.ent.gz | 252 KB | Display | PDB format |
PDBx/mmJSON format | 5ah4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ah/5ah4 ftp://data.pdbj.org/pub/pdb/validation_reports/ah/5ah4 | HTTPS FTP |
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-Related structure data
Related structure data | 5aguC 5agvC 5ah2C 3p16S 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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.98634, 0.04807, 0.15753), Vector: |
-Components
#1: Protein | Mass: 41692.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC(2)155 / Plasmid: PVP008_DNANMSM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QND6, DNA-directed DNA polymerase #2: Protein/peptide | Type: Peptide-like / Class: Antibiotic / Mass: 1197.593 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) STREPTOMYCES CAELICUS (bacteria) / References: BIRD: PRD_002466 #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | Compound details | Novel synthetic analog of natural product Griselimycin | Nonpolymer details | CYCLOHEXYLGRISELIMYCIN IS A SYNTHETICALLY GENERATED DERIVATIVE OF THE NATURAL PRODUCT GRISELIMYCIN ...CYCLOHEXYL | Sequence details | FIRST 4 N-TERMINAL RESIDUES REMAINED FROM THE TEV SITE AFTER PROTEOLYTI | |
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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: 3.08 Å3/Da / Density % sol: 60.1 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 200 MM MGCL2 16.3 % (V/V) GLYCEROL 12.2 % (W/V) PEG 3350 100 MM TRIS-HCL PH 7.44 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 22, 2013 / Details: MIRRORS |
Radiation | Monochromator: BARTELS MONOCHROMATOR WITH DUAL CHANNEL CUT CRYSTALS Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→76.27 Å / Num. obs: 47835 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 47.59 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.31→2.32 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3P16 Resolution: 2.313→76.271 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 24 / Stereochemistry target values: ML / Details: WEAKLY DEFINED RESIDUES WERE MODELLED AS ALANINES.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.313→76.271 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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