+Open data
-Basic information
Entry | Database: PDB / ID: 1gku | ||||||
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Title | Reverse gyrase from Archaeoglobus fulgidus | ||||||
Components | REVERSE GYRASE | ||||||
Keywords | TOPOISOMERASE / DNA SUPERCOILING / ARCHAEA / HELICASE | ||||||
Function / homology | Function and homology information Isomerases; Isomerases altering macromolecular conformation; Enzymes altering nucleic acid conformation / reverse gyrase activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA unwinding involved in DNA replication / DNA topological change / helicase activity / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ARCHAEOGLOBUS FULGIDUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å | ||||||
Authors | Rodriguez, A.C. / Stock, D. | ||||||
Citation | Journal: Embo J. / Year: 2002 Title: Crystal Structure of Reverse Gyrase: Insights Into the Positive Supercoiling of DNA. Authors: Rodriguez, A.C. / Stock, D. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gku.cif.gz | 213.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gku.ent.gz | 174.2 KB | Display | PDB format |
PDBx/mmJSON format | 1gku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/1gku ftp://data.pdbj.org/pub/pdb/validation_reports/gk/1gku | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 120141.164 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Strain: VC-16 / Description: GERMAN COLLECTION OF MICROORGANISMS (DSMZ) / Plasmid: PRET3A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: O29238 |
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#2: Water | ChemComp-HOH / |
Compound details | CHAIN B ENGINEERED MUTATION PRO719LEU, LEU1046MET. NINETEEN RESIDUES N-TERMINAL TO SERINE 33 IN THE ...CHAIN B ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: 15% PEG 1000, 15% ETHYLENE GLYCOL, 100 MM CACODYLATE (PH 6) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion, sitting 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: ESRF / Beamline: ID14-4 / Wavelength: 0.9686 |
Detector | Type: ADSC / Date: Feb 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→41 Å / Num. obs: 28735 / % possible obs: 99.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 67.6 Å2 / Rsym value: 0.062 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.7→2.78 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.288 / % possible all: 99.3 |
Reflection | *PLUS Lowest resolution: 41 Å / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 99.3 % / Rmerge(I) obs: 0.288 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.7→41 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF Details: NINETEEN RESIDUES N-TERMINAL TO SERINE 33 IN THE COORDINATES HAVE BEEN MODELLED AS THREE NON- CONTIGUOUS CHAINS OF POLYALANINE. AMINO ACID SEQUENCE AND NUMBERING FOR THESE RESIDUES HAS BEEN ...Details: NINETEEN RESIDUES N-TERMINAL TO SERINE 33 IN THE COORDINATES HAVE BEEN MODELLED AS THREE NON- CONTIGUOUS CHAINS OF POLYALANINE. AMINO ACID SEQUENCE AND NUMBERING FOR THESE RESIDUES HAS BEEN ASSIGNED AS 1-21. THEIR ACTUAL POSITION IN THE PROTEIN SEQUENCE IS UNCLEAR DUE TO POOR ELECTRON DENSITY.
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Solvent computation | Bsol: 66.5478 Å2 / ksol: 0.35335 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.8 Å / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: WATER_REP.PARAM / Topol file: WATER.TOP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 41 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |