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- PDB-1gl9: Archaeoglobus fulgidus reverse gyrase complexed with ADPNP -

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Basic information

Entry
Database: PDB / ID: 1gl9
TitleArchaeoglobus fulgidus reverse gyrase complexed with ADPNP
ComponentsREVERSE GYRASE
KeywordsTOPOISOMERASE / 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
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 / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Single Sheet / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Reverse gyrase
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 30, 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 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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

Downloads & links

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Assembly

Deposited unit
B: REVERSE GYRASE
C: REVERSE GYRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,1316
Polymers243,0702
Non-polymers1,0614
Water0
1
B: REVERSE GYRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,0663
Polymers121,5351
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: REVERSE GYRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,0663
Polymers121,5351
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)132.410, 68.690, 134.000
Angle α, β, γ (deg.)90.00, 99.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.98909, -0.06165, -0.13379), (0.06839, 0.99658, 0.04638), (0.13047, -0.05502, 0.98992)
Vector: -7.58849, -11.07901, 31.31255)

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Components

#1: Protein REVERSE GYRASE / / TOP-RG


Mass: 121535.023 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ADENYLYLIMIDODIPHOSPHATE (ADPNP) / 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: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Compound detailsCHAIN B ENGINEERED MUTATION PRO719LEU, LEU1046MET. RESIDUES N-TERMINAL TO B31 IN MOLECULE B, AND TO ...CHAIN B ENGINEERED MUTATION PRO719LEU, LEU1046MET. RESIDUES N-TERMINAL TO B31 IN MOLECULE B, AND TO RESIDUE C32 IN MOLECULE C HAVE BEEN MODELLED AS POLYALANINE. THEIR IDENTITY AND NUMBERING IN THE PROTEIN SEQUENCE IS ARBITRARY.

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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: 2.44 Å3/Da / Density % sol: 58.7 %
Crystal growpH: 6
Details: 15% PEG 1000, 15% ETHYLENE GLYCOL 100 MM CACODYLATE (PH 6),2MM ADPNP
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
8100 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: 3.2→34 Å / Num. obs: 38400 / % possible obs: 96.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 81 Å2 / Rsym value: 0.102 / Net I/σ(I): 5.2
Reflection shellResolution: 3.2→3.35 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.321 / % possible all: 96.7
Reflection
*PLUS
Lowest resolution: 34 Å / Num. obs: 38401 / Rmerge(I) obs: 0.102
Reflection shell
*PLUS
% possible obs: 96.7 % / Rmerge(I) obs: 0.321

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GKU

1gku


Resolution: 3.2→34 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
Details: RESIDUES N-TERMINAL TO B31 IN MOLECULE B, AND TO RESIDUE C32 IN MOLECULE C HAVE BEEN MODELLED AS POLYALANINE. THEIR IDENTITY AND NUMBERING IN THE PROTEIN SEQUENCE IS ARBITRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.332 1916 4.8 %RANDOM
Rwork0.256 ---
obs0.256 38400 96.6 %-
Solvent computationBsol: 59.5563 Å2 / ksol: 0.285991 e/Å3
Displacement parametersBiso mean: 75.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.642 Å20 Å2-27.593 Å2
2--9.01 Å20 Å2
3----4.367 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 3.2→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16334 0 64 0 16398
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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
X-RAY DIFFRACTIONc_mcangle_it4
X-RAY DIFFRACTIONc_scbond_it4
X-RAY DIFFRACTIONc_scangle_it6
Refine LS restraints NCSWeight Biso : 10 / Weight position: 15
LS refinement shellResolution: 3.2→3.31 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.385 209 5.3 %
Rwork0.326 3494 -
obs--93.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4ANP_XPLOR_PAR.TXT
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 34 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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