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- PDB-1gku: Reverse gyrase from Archaeoglobus fulgidus -

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Basic information

Entry
Database: PDB / ID: 1gku
TitleReverse gyrase from Archaeoglobus fulgidus
ComponentsREVERSE GYRASE
KeywordsTOPOISOMERASE / DNA SUPERCOILING / ARCHAEA / HELICASE
Function / homology
Function and homology information


reverse gyrase activity / Isomerases; Isomerases altering macromolecular conformation; Enzymes altering nucleic acid conformation / DNA negative supercoiling activity / DNA topological change / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / ATP hydrolysis activity / DNA binding ...reverse gyrase activity / Isomerases; Isomerases altering macromolecular conformation; Enzymes altering nucleic acid conformation / DNA negative supercoiling activity / DNA topological change / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / 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 / Reverse gyrase / Reverse gyrase, TOPRIM domain / Zinc finger reverse gyrase N-terminal-type profile. / Zinc finger reverse gyrase C-terminal-type profile. / EV matrix protein fold / Topoisomerase I; domain 2 / Topoisomerase I, domain 2 ...reverse gyrase domain / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 - #120 / EV matrix protein fold - #20 / Reverse gyrase / Reverse gyrase, TOPRIM domain / Zinc finger reverse gyrase N-terminal-type profile. / Zinc finger reverse gyrase C-terminal-type profile. / EV matrix protein fold / Topoisomerase I; domain 2 / Topoisomerase I, domain 2 / Rossmann fold - #140 / Topoisomerase I; domain 4 / Topoisomerase I, domain 4 / Anthopleurin-A / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / Topoisomerase (Topo) IA-type catalytic domain profile. / 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 / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain / Single Sheet / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsRodriguez, A.C. / Stock, D.
CitationJournal: Embo J. / Year: 2002
Title: Crystal Structure of Reverse Gyrase: Insights Into the Positive Supercoiling of DNA.
Authors: Rodriguez, A.C. / Stock, D.
History
DepositionAug 21, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: REVERSE GYRASE


Theoretical massNumber of molelcules
Total (without water)120,1411
Polymers120,1411
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)65.198, 67.985, 129.728
Angle α, β, γ (deg.)90.00, 104.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein REVERSE GYRASE / TOP-RG


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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN 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.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 52 %
Crystal growpH: 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
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris-HCl1droppH8.0
2200 mM1dropNaCl
310 mM1dropMgCl2
41 mMEDTA1drop
50.02 %1dropNaN3
610 mg/mlprotein1drop
715 %PEG10001reservoir
815 %ethylene glycol1reservoir
9100 mMcacodylate1reservoirpH6.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9686
DetectorType: ADSC / Date: Feb 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVE/RESOLVEphasing
RefinementMethod 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1474 4.8 %RANDOM
Rwork0.226 ---
obs0.226 30333 99.3 %-
Solvent computationBsol: 66.5478 Å2 / ksol: 0.35335 e/Å3
Displacement parametersBiso mean: 55.4 Å2
Baniso -1Baniso -2Baniso -3
1-7.13 Å20 Å20.438 Å2
2---7.426 Å20 Å2
3---0.296 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.7→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8151 0 0 157 8308
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.423
X-RAY DIFFRACTIONc_mcangle_it5.774
X-RAY DIFFRACTIONc_scbond_it5.284
X-RAY DIFFRACTIONc_scangle_it8.116
LS refinement shellResolution: 2.7→2.8 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.329 18 0.6 %
Rwork0.253 2961 -
obs--99.3 %
Xplor fileSerial 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

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