[English] 日本語
Yorodumi- PDB-2xkj: CRYSTAL STRUCTURE OF CATALYTIC CORE OF A. BAUMANNII TOPO IV (PARE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xkj | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF CATALYTIC CORE OF A. BAUMANNII TOPO IV (PARE- PARC FUSION TRUNCATE) | ||||||
Components | TOPOISOMERASE IV | ||||||
Keywords | ISOMERASE / TYPE IIA TOPOISOMERASE | ||||||
Function / homology | Function and homology information DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / extrinsic component of plasma membrane / DNA topological change / chromosome segregation / chromosome / DNA binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ACINETOBACTER BAUMANNII (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Wohlkonig, A. / Chan, P.F. / Fosberry, A.P. / Homes, P. / Huang, J. / Kranz, M. / Leydon, V.R. / Miles, T.J. / Pearson, N.D. / Perera, R.L. ...Wohlkonig, A. / Chan, P.F. / Fosberry, A.P. / Homes, P. / Huang, J. / Kranz, M. / Leydon, V.R. / Miles, T.J. / Pearson, N.D. / Perera, R.L. / Shillings, A.J. / Gwynn, M.N. / Bax, B.D. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Structural Basis of Quinolone Inhibition of Type Iia Topoisomerases and Target-Mediated Resistance Authors: Wohlkonig, A. / Chan, P.F. / Fosberry, A.P. / Homes, P. / Huang, J. / Kranz, M. / Leydon, V.R. / Miles, T.J. / Pearson, N.D. / Perera, R.L. / Shillings, A.J. / Gwynn, M.N. / Bax, B.D. | ||||||
History |
| ||||||
Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2xkj.cif.gz | 171.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2xkj.ent.gz | 132.1 KB | Display | PDB format |
PDBx/mmJSON format | 2xkj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xkj_validation.pdf.gz | 453.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2xkj_full_validation.pdf.gz | 461.8 KB | Display | |
Data in XML | 2xkj_validation.xml.gz | 31.9 KB | Display | |
Data in CIF | 2xkj_validation.cif.gz | 47.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xk/2xkj ftp://data.pdbj.org/pub/pdb/validation_reports/xk/2xkj | HTTPS FTP |
-Related structure data
Related structure data | 2xkkC 2xcsS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
| ||||||||
Details | DIMER SITS ON CRYSTALLOGRAPHIC TWO FOLD AXIS. |
-Components
#1: Protein | Mass: 86085.773 Da / Num. of mol.: 1 Fragment: PARE SUBUNIT C-TERMINAL 28KDA DOMAIN, RESIDUES 370-627, PARC SUBUNIT N-TERMINAL 58KDA DOMAIN, RESIDUES 1 TO 503 Source method: isolated from a genetically manipulated source Details: THE CONSTRUCT IS A FUSION OF THE TOPO IV, PARE AND PARC SUBUNITS. RESIDUE 604 OF PARE IS LINKED TO RESIDUES 996 OF PARC Source: (gene. exp.) ACINETOBACTER BAUMANNII (bacteria) / Strain: EUROFINS MEDINET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0V9T6, UniProt: B0VP98, EC: 5.99.1.- | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.36 % / Description: NONE |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop Details: HANGING DROP VAPOUR DIFFUSION METHOD USING 0.2 M LITHIUM SULFATE, 0.1 M TRIS PH 8.5, 16% PEG 4000 AS THE PRECIPITATING AGENT |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9755 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9755 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 46394 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 26.56 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.5 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DOMAINS FROM PDB ENTRY 2XCS Resolution: 2.2→24.909 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 20.69 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.337 Å2 / ksol: 0.331 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→24.909 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|