- PDB-1gku: Reverse gyrase from Archaeoglobus fulgidus -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 1gku
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 / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / cytoplasm Similarity search - Function
reverse gyrase domain / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #120 / EV matrix protein fold - #20 / EV matrix protein fold / Reverse gyrase / Reverse gyrase, TOPRIM domain / Zinc finger reverse gyrase N-terminal-type profile. / Zinc finger reverse gyrase C-terminal-type profile. / Topoisomerase I; domain 2 / Topoisomerase I, domain 2 ...reverse gyrase domain / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #120 / EV matrix protein fold - #20 / EV matrix protein fold / Reverse gyrase / Reverse gyrase, TOPRIM domain / Zinc finger reverse gyrase N-terminal-type profile. / Zinc finger reverse gyrase C-terminal-type profile. / Topoisomerase I; domain 2 / Topoisomerase I, domain 2 / Rossmann fold - #140 / Topoisomerase I; domain 4 / Topoisomerase I, domain 4 / Topoisomerase (Topo) IA-type catalytic domain profile. / Anthopleurin-A / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central / DNA topoisomerase, type IA, central region, subdomain 1 / DNA topoisomerase, type IA, central region, subdomain 3 / DNA topoisomerase, type IA, core domain / DNA topoisomerase / Bacterial DNA topoisomeraes I ATP-binding domain / Bacterial DNA topoisomerase I DNA-binding domain / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain / Single Sheet / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
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.
Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Compound details
CHAIN B ENGINEERED MUTATION PRO719LEU, LEU1046MET. NINETEEN RESIDUES N-TERMINAL TO SERINE 33 IN THE ...CHAIN B ENGINEERED MUTATION PRO719LEU, LEU1046MET. 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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Experimental details
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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 %
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
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Processing
Software
Name
Version
Classification
CNS
1
refinement
MOSFLM
datareduction
SCALA
datascaling
SOLVE/RESOLVE
phasing
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.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.295
1474
4.8 %
RANDOM
Rwork
0.226
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obs
0.226
30333
99.3 %
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Solvent computation
Bsol: 66.5478 Å2 / ksol: 0.35335 e/Å3
Displacement parameters
Biso mean: 55.4 Å2
Baniso -1
Baniso -2
Baniso -3
1-
7.13 Å2
0 Å2
0.438 Å2
2-
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-7.426 Å2
0 Å2
3-
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0.296 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.49 Å
0.34 Å
Luzzati d res low
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5 Å
Luzzati sigma a
0.45 Å
0.23 Å
Refinement step
Cycle: LAST / Resolution: 2.7→41 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
8151
0
0
157
8308
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
X-RAY DIFFRACTION
c_bond_d
0.007
X-RAY DIFFRACTION
c_bond_d_na
X-RAY DIFFRACTION
c_bond_d_prot
X-RAY DIFFRACTION
c_angle_d
X-RAY DIFFRACTION
c_angle_d_na
X-RAY DIFFRACTION
c_angle_d_prot
X-RAY DIFFRACTION
c_angle_deg
1.3
X-RAY DIFFRACTION
c_angle_deg_na
X-RAY DIFFRACTION
c_angle_deg_prot
X-RAY DIFFRACTION
c_dihedral_angle_d
X-RAY DIFFRACTION
c_dihedral_angle_d_na
X-RAY DIFFRACTION
c_dihedral_angle_d_prot
X-RAY DIFFRACTION
c_improper_angle_d
X-RAY DIFFRACTION
c_improper_angle_d_na
X-RAY DIFFRACTION
c_improper_angle_d_prot
X-RAY DIFFRACTION
c_mcbond_it
3.42
3
X-RAY DIFFRACTION
c_mcangle_it
5.77
4
X-RAY DIFFRACTION
c_scbond_it
5.28
4
X-RAY DIFFRACTION
c_scangle_it
8.11
6
LS refinement shell
Resolution: 2.7→2.8 Å / Total num. of bins used: 10
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