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- PDB-5zxm: Crystal Structure of GyraseB N-terminal at 1.93A Resolution -

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Basic information

Entry
Database: PDB / ID: 5zxm
TitleCrystal Structure of GyraseB N-terminal at 1.93A Resolution
ComponentsDNA gyrase subunit B
KeywordsISOMERASE / Topoisomerase / ATP binding domain / GyrB-NTD
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site ...DNA gyrase subunit B insert domain / DNA gyrase B subunit insert domain / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Toprim domain profile. / TOPRIM domain / Ribosomal Protein S5; domain 2 / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / DNA gyrase subunit B
Similarity search - Component
Biological speciesSalmonella enterica I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.938 Å
AuthorsTiwari, P. / Gupta, D. / Sachdeva, E. / Sharma, S. / Singh, T.P. / Ethayathulla, A.S. / Kaur, P.
CitationJournal: Arch.Biochem.Biophys. / Year: 2021
Title: Structural insights into the transient closed conformation and pH dependent ATPase activity of S.Typhi GyraseB N- terminal domain.
Authors: Gupta, D. / Tiwari, P. / Haque, M.A. / Sachdeva, E. / Hassan, M.I. / Ethayathulla, A.S. / Kaur, P.
History
DepositionMay 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 15, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / computing ...atom_site / computing / diffrn / entity / entity_name_com / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_validate_main_chain_plane / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns_shell / software / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _diffrn.pdbx_serial_crystal_experiment / _entity.pdbx_ec ..._diffrn.pdbx_serial_crystal_experiment / _entity.pdbx_ec / _entity.pdbx_number_of_molecules / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_strain / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.pdbx_R_Free_selection_details / _refine.pdbx_ls_cross_valid_method / _refine_hist.cycle_id / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_residues_total / _reflns_shell.number_unique_obs / _software.name / _software.version / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Description: Model orientation/position
Details: one of the magnesium ion was replaced by water. An alternate conformation for Gly114/B was deleted.
Provider: author / Type: Coordinate replacement
Revision 2.1Mar 10, 2021Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _software.name
Revision 2.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA gyrase subunit B
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,05712
Polymers88,4832
Non-polymers1,57310
Water10,088560
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-78 kcal/mol
Surface area30730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.420, 86.530, 135.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA gyrase subunit B /


Mass: 44241.742 Da / Num. of mol.: 2 / Fragment: N-terminal Domain / Mutation: V40A, E85S, H173K, E174S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica I (bacteria) / Gene: gyrB / Plasmid: pET-28 a (+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A3R0U328, DNA topoisomerase (ATP-hydrolysing)

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Non-polymers , 6 types, 570 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 560 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.64 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 3350, lithium sulfate, ATP, Tris, pH 8.0

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.938→73.004 Å / Num. obs: 69892 / % possible obs: 99.3 % / Redundancy: 4.5 % / Biso Wilson estimate: 29.2 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.101 / Rsym value: 0.074 / Net I/σ(I): 10.3
Reflection shellResolution: 1.94→1.97 Å / Rmerge(I) obs: 0.8 / Num. unique obs: 3436 / CC1/2: 0.67 / Rsym value: 0.5

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Processing

Software
NameVersionClassification
REFMAC5.5refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EI1

1ei1


Resolution: 1.938→73.004 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 1458 2.09 %RANDOM
Rwork0.1815 ---
obs0.1824 69818 99.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.07 Å2 / Biso mean: 34.9806 Å2 / Biso min: 14.24 Å2
Refinement stepCycle: final / Resolution: 1.938→73.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6032 0 98 560 6690
Biso mean--30.6 39.56 -
Num. residues----780
LS refinement shellResolution: 1.94→2 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.36 1458 -
Rwork0.31 3436 -
obs--99 %

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