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Yorodumi- PDB-1aj6: NOVOBIOCIN-RESISTANT MUTANT (R136H) OF THE N-TERMINAL 24 KDA FRAG... -
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-Basic information
Entry | Database: PDB / ID: 1aj6 | ||||||
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Title | NOVOBIOCIN-RESISTANT MUTANT (R136H) OF THE N-TERMINAL 24 KDA FRAGMENT OF DNA GYRASE B COMPLEXED WITH NOVOBIOCIN AT 2.3 ANGSTROMS RESOLUTION | ||||||
Components | GYRASE | ||||||
Keywords | TOPOISOMERASE / GYRASE / NOVOBIOCIN / ANTIBIOTIC / RESISTANT MUTANT | ||||||
Function / homology | Function and homology information DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus / response to antibiotic ...DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / ATP-dependent activity, acting on DNA / DNA-templated DNA replication / chromosome / response to xenobiotic stimulus / response to antibiotic / DNA-templated transcription / DNA binding / ATP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.3 Å | ||||||
Authors | Weston, S.A. / Tunnicliffe, A. / Pauptit, R.A. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: The entropic penalty of ordered water accounts for weaker binding of the antibiotic novobiocin to a resistant mutant of DNA gyrase: a thermodynamic and crystallographic study. Authors: Holdgate, G.A. / Tunnicliffe, A. / Ward, W.H. / Weston, S.A. / Rosenbrock, G. / Barth, P.T. / Taylor, I.W. / Pauptit, R.A. / Timms, D. #1: Journal: To be Published Title: Antibacterial Design Based on the Structures of Gyrase-Inhibitor Complexes Authors: Pauptit, R.A. / Weston, S.A. / Breeze, A.L. / Derbyshire, D.J. / Tucker, A.D. / Hales, N. / Hollinshead, D. / Timms, D. #2: Journal: Proteins / Year: 1997 Title: The High-Resolution Crystal Structure of a 24-kDa Gyrase B Fragment from E. Coli Complexed with One of the Most Potent Coumarin Inhibitors, Clorobiocin Authors: Tsai, F.T. / Singh, O.M. / Skarzynski, T. / Wonacott, A.J. / Weston, S. / Tucker, A. / Pauptit, R.A. / Breeze, A.L. / Poyser, J.P. / O'Brien, R. / Ladbury, J.E. / Wigley, D.B. #3: Journal: Embo J. / Year: 1996 Title: The Nature of Inhibition of DNA Gyrase by the Coumarins and the Cyclothialidines Revealed by X-Ray Crystallography Authors: Lewis, R.J. / Singh, O.M. / Smith, C.V. / Skarzynski, T. / Maxwell, A. / Wonacott, A.J. / Wigley, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aj6.cif.gz | 54.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aj6.ent.gz | 38.2 KB | Display | PDB format |
PDBx/mmJSON format | 1aj6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1aj6_validation.pdf.gz | 730.5 KB | Display | wwPDB validaton report |
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Full document | 1aj6_full_validation.pdf.gz | 739 KB | Display | |
Data in XML | 1aj6_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 1aj6_validation.cif.gz | 15.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/1aj6 ftp://data.pdbj.org/pub/pdb/validation_reports/aj/1aj6 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24040.936 Da / Num. of mol.: 1 / Fragment: N-TERMINAL 24 KDA / Mutation: R136H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Description: PLASMID PTB382 ENCODING MUTANT DERIVED FROM PAM24 WHICH ENCODES 24 KDA SUBDOMAIN (SUPPLIED BY A. MAXWELL, LEICESTER), WHICH IN TURN WAS DERIVED FROM PAG111 PLASMID WHICH ENCODES FOR GYRB Cellular location: CYTOPLASM / Gene: GYRB / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): MM294 References: UniProt: P06982, UniProt: P0AES6*PLUS, EC: 5.99.1.3 |
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#2: Chemical | ChemComp-NOV / |
#3: Water | ChemComp-HOH / |
Compound details | THE MUTATED RESIDUE HIS 136 HAS AN UNUSUAL ECLIPSED SIDE CHAIN CONFORMATION WHICH IS STABILISED BY ...THE MUTATED RESIDUE HIS 136 HAS AN UNUSUAL ECLIPSED SIDE CHAIN CONFORMATI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 45 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.2 Details: HANGING DROP VAPOR DIFFUSION; 12MGS/ML PROTEIN/NOVOBIOCIN MIXED WITH EQUAL VOLUME OF RESERVOIR SOLUTION (12% V/V PEG200, 100MM MES PH6.2), vapor diffusion - hanging drop | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
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: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996 / Details: VERTICALLY FOCUSSED PT-COATED MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→19.8 Å / Num. obs: 9455 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.131 / Mean I/σ(I) obs: 5.6 / Rsym value: 0.131 / % possible all: 97 |
Reflection | *PLUS Num. measured all: 48291 |
Reflection shell | *PLUS % possible obs: 97 % |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: WILD-TYPE 24KDA FRAGMENT/NOVOBIOCIN COMPLEX Resolution: 2.3→19.8 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROGEO Details: STRAINED GEOMETRY AND DIFFERENCE DENSITY AT PRO 23 SUGGEST IT MIGHT HAVE MORE THAN ONE CONFORMATION. ASN 178 IS IN A DISALLOWED REGION OF THE RAMACHANDRAN PLOT. IT ADOPTS A CLASSICAL C-7 ...Details: STRAINED GEOMETRY AND DIFFERENCE DENSITY AT PRO 23 SUGGEST IT MIGHT HAVE MORE THAN ONE CONFORMATION. ASN 178 IS IN A DISALLOWED REGION OF THE RAMACHANDRAN PLOT. IT ADOPTS A CLASSICAL C-7 AXIAL CONFORMATION TYPICAL OF GLYCINE RESIDUES WITH A CO(N-1)..N(N+1) H-BOND.
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Solvent computation | Solvent model: TNT / Bsol: 241 Å2 / ksol: 1 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→19.8 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5D / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.195 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.015 / Weight: 10 | ||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.4 Å / Rfactor Rfree: 0.132 / Rfactor obs: 0.23 |