[English] 日本語
Yorodumi- PDB-1mw9: Crystal Structure of H365R mutant of 67 kDA N-terminal fragment o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mw9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of H365R mutant of 67 kDA N-terminal fragment of E. coli DNA Topoisomerase I | ||||||
Components | DNA Topoisomerase I | ||||||
Keywords | ISOMERASE / DNA TOPOISOMERASE / DECATENASE ENZYME / TOPRIM DOMAIN | ||||||
Function / homology | Function and homology information DNA topoisomerase activity / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / chromosome / DNA binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Perry, K. / Mondragon, A. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Structure of a Complex between E. coli DNA Topoisomerase I and Single-Stranded DNA. Authors: Perry, K. / Mondragon, A. #1: Journal: Nature / Year: 1994 Title: Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I Authors: Lima, C.D. / Wang, J.C. / Mondragon, A. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE THE AUTHOR'S SEQUENCE HAS ASN AT POSITION 549, WHICH HAS BEEN CONFIRMED BY SEQUENCING THE GENE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1mw9.cif.gz | 138.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1mw9.ent.gz | 108.8 KB | Display | PDB format |
PDBx/mmJSON format | 1mw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mw/1mw9 ftp://data.pdbj.org/pub/pdb/validation_reports/mw/1mw9 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1mw8C 1eclS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 66930.812 Da / Num. of mol.: 1 / Fragment: 67 kDa N-terminal fragment / Mutation: H365R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: TopA / Plasmid: pGEX-4T / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P06612, DNA topoisomerase | ||
---|---|---|---|
#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.31 % |
---|---|
Crystal grow | Temperature: 287 K / Method: dialysis / pH: 8 / Details: ammonium sulfate, pH 8, DIALYSIS, temperature 287K |
Crystal grow | *PLUS Method: vapor diffusion, hanging drop |
Components of the solutions | *PLUS Conc.: 2.1 M / Common name: ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 103 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→50 Å / Num. all: 80202 / Num. obs: 79717 / % possible obs: 98.4 % / Observed criterion σ(I): 10737.6 / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.055 / Net I/σ(I): 8.2 |
Reflection | *PLUS Num. measured all: 398050 / Rmerge(I) obs: 0.057 |
Reflection shell | *PLUS % possible obs: 98.4 % / Rmerge(I) obs: 0.407 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ECL Resolution: 1.67→49.39 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.785 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.686 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.67→49.39 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.67→1.713 Å / Rfactor Rfree error: 0.11 / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Version: 5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / Num. reflection obs: 75619 / Num. reflection Rfree: 4024 / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.205 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|