+Open data
-Basic information
Entry | Database: PDB / ID: 1ab4 | ||||||
---|---|---|---|---|---|---|---|
Title | 59KDA FRAGMENT OF GYRASE A FROM E. COLI | ||||||
Components | GYRASE A | ||||||
Keywords | TOPOISOMERASE / TOPOISOMERASE II / GYRASE / SUPERCOILING DNA | ||||||
Function / homology | Function and homology information DNA gyrase complex / negative regulation of DNA-templated DNA replication / 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 ...DNA gyrase complex / negative regulation of DNA-templated DNA replication / 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 / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.8 Å | ||||||
Authors | Cabral, J.H.M. / Maxwell, A. / Liddington, R.C. | ||||||
Citation | Journal: Nature / Year: 1997 Title: Crystal structure of the breakage-reunion domain of DNA gyrase. Authors: Cabral, J.H. / Jackson, A.P. / Smith, C.V. / Shikotra, N. / Maxwell, A. / Liddington, R.C. #1: Journal: Nature / Year: 1996 Title: Structure and Mechanism of DNA Topoisomerase II Authors: Berger, J.M. / Gamblin, S.J. / Harrison, S.C. / Wang, J.C. #2: Journal: Nature / Year: 1996 Title: Erratum. Structure and Mechanism of DNA Topoisomerase II Authors: Berger, J.M. / Gamblin, S.J. / Harrison, S.C. / Wang, J.C. #3: Journal: Crit.Rev.Biochem.Mol.Biol. / Year: 1991 Title: DNA Gyrase: Structure and Function Authors: Reece, R.J. / Maxwell, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ab4.cif.gz | 97.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ab4.ent.gz | 75.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ab4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ab4_validation.pdf.gz | 424.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ab4_full_validation.pdf.gz | 433.8 KB | Display | |
Data in XML | 1ab4_validation.xml.gz | 19 KB | Display | |
Data in CIF | 1ab4_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ab/1ab4 ftp://data.pdbj.org/pub/pdb/validation_reports/ab/1ab4 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 55381.398 Da / Num. of mol.: 1 / Fragment: 59KDA FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) References: UniProt: P09097, UniProt: P0AES4*PLUS, EC: 5.99.1.3 |
---|---|
#2: Water | ChemComp-HOH / |
Compound details | TYROSINE 122 IS INVOLVED IN THE TRANSESTER |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 8.5 Details: PROTEIN WAS CRYSTALLISED FROM 8% PEG 8000, 0.02M NACL 0.1 M TRIS PH8.5. | ||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: unknown | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Apr 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→15 Å / Num. obs: 16475 / % possible obs: 100 % / Redundancy: 7 % / Rsym value: 0.047 / Net I/σ(I): 20 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 6 % / Mean I/σ(I) obs: 10 / Rsym value: 0.156 / % possible all: 100 |
Reflection | *PLUS Rmerge(I) obs: 0.047 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIR / Resolution: 2.8→15 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUPED RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT CORRECTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.93 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.31 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|