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- PDB-2xkj: CRYSTAL STRUCTURE OF CATALYTIC CORE OF A. BAUMANNII TOPO IV (PARE... -

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Basic information

Entry
Database: PDB / ID: 2xkj
TitleCRYSTAL STRUCTURE OF CATALYTIC CORE OF A. BAUMANNII TOPO IV (PARE- PARC FUSION TRUNCATE)
ComponentsTOPOISOMERASE IV
KeywordsISOMERASE / TYPE IIA TOPOISOMERASE
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / extrinsic component of plasma membrane / DNA topological change / chromosome segregation / chromosome / DNA binding / ATP binding / cytoplasm
Similarity search - Function
DNA topoisomerase IV, subunit A, Gram-negative / DNA topoisomerase IV, subunit B, Gram-negative / Rossmann fold - #670 / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A ...DNA topoisomerase IV, subunit A, Gram-negative / DNA topoisomerase IV, subunit B, Gram-negative / Rossmann fold - #670 / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / 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 / Toprim domain profile. / TOPRIM domain / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA topoisomerase 4 subunit B / DNA topoisomerase 4 subunit A
Similarity search - Component
Biological speciesACINETOBACTER BAUMANNII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWohlkonig, A. / Chan, P.F. / Fosberry, A.P. / Homes, P. / Huang, J. / Kranz, M. / Leydon, V.R. / Miles, T.J. / Pearson, N.D. / Perera, R.L. ...Wohlkonig, A. / Chan, P.F. / Fosberry, A.P. / Homes, P. / Huang, J. / Kranz, M. / Leydon, V.R. / Miles, T.J. / Pearson, N.D. / Perera, R.L. / Shillings, A.J. / Gwynn, M.N. / Bax, B.D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Structural Basis of Quinolone Inhibition of Type Iia Topoisomerases and Target-Mediated Resistance
Authors: Wohlkonig, A. / Chan, P.F. / Fosberry, A.P. / Homes, P. / Huang, J. / Kranz, M. / Leydon, V.R. / Miles, T.J. / Pearson, N.D. / Perera, R.L. / Shillings, A.J. / Gwynn, M.N. / Bax, B.D.
History
DepositionJul 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1May 19, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Sep 25, 2019Group: Data collection / Other / Category: pdbx_database_status / reflns
Item: _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: TOPOISOMERASE IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3704
Polymers86,0861
Non-polymers2843
Water9,620534
1
E: TOPOISOMERASE IV
hetero molecules

E: TOPOISOMERASE IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,7408
Polymers172,1722
Non-polymers5686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7170 Å2
ΔGint-38.2 kcal/mol
Surface area61590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.389, 74.433, 80.211
Angle α, β, γ (deg.)90.00, 107.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-3081-

HOH

DetailsDIMER SITS ON CRYSTALLOGRAPHIC TWO FOLD AXIS.

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Components

#1: Protein TOPOISOMERASE IV /


Mass: 86085.773 Da / Num. of mol.: 1
Fragment: PARE SUBUNIT C-TERMINAL 28KDA DOMAIN, RESIDUES 370-627, PARC SUBUNIT N-TERMINAL 58KDA DOMAIN, RESIDUES 1 TO 503
Source method: isolated from a genetically manipulated source
Details: THE CONSTRUCT IS A FUSION OF THE TOPO IV, PARE AND PARC SUBUNITS. RESIDUE 604 OF PARE IS LINKED TO RESIDUES 996 OF PARC
Source: (gene. exp.) ACINETOBACTER BAUMANNII (bacteria) / Strain: EUROFINS MEDINET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B0V9T6, UniProt: B0VP98, EC: 5.99.1.-
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 534 / Source method: isolated from a natural source / Formula: H2O

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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: 2.69 Å3/Da / Density % sol: 54.36 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop
Details: HANGING DROP VAPOUR DIFFUSION METHOD USING 0.2 M LITHIUM SULFATE, 0.1 M TRIS PH 8.5, 16% PEG 4000 AS THE PRECIPITATING AGENT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9755
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9755 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 46394 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 26.56 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 13.7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKLdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DOMAINS FROM PDB ENTRY 2XCS

2xcs


Resolution: 2.2→24.909 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 20.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2129 2342 5.1 %
Rwork0.1608 --
obs0.1634 46360 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.337 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso mean: 30.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.2682 Å20 Å2-0.8283 Å2
2--0.9214 Å20 Å2
3---1.3469 Å2
Refinement stepCycle: LAST / Resolution: 2.2→24.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5628 0 16 534 6178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085896
X-RAY DIFFRACTIONf_angle_d1.098002
X-RAY DIFFRACTIONf_dihedral_angle_d17.5722252
X-RAY DIFFRACTIONf_chiral_restr0.07908
X-RAY DIFFRACTIONf_plane_restr0.0041054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2027-2.24760.28721140.18912562X-RAY DIFFRACTION98
2.2476-2.29650.28271320.18822592X-RAY DIFFRACTION100
2.2965-2.34990.25711530.18232556X-RAY DIFFRACTION100
2.3499-2.40860.26081170.18172573X-RAY DIFFRACTION100
2.4086-2.47360.23991370.17692597X-RAY DIFFRACTION100
2.4736-2.54640.24271500.16562566X-RAY DIFFRACTION100
2.5464-2.62850.22761640.17352545X-RAY DIFFRACTION100
2.6285-2.72230.24421190.16722621X-RAY DIFFRACTION100
2.7223-2.83110.20731470.16522559X-RAY DIFFRACTION100
2.8311-2.95980.2171270.16222614X-RAY DIFFRACTION100
2.9598-3.11560.23261400.16872578X-RAY DIFFRACTION100
3.1156-3.31040.21061440.16722589X-RAY DIFFRACTION100
3.3104-3.56530.21511490.15732572X-RAY DIFFRACTION100
3.5653-3.92280.1841460.14392610X-RAY DIFFRACTION100
3.9228-4.48760.1521350.12682588X-RAY DIFFRACTION100
4.4876-5.6430.1911260.13832636X-RAY DIFFRACTION100
5.643-24.91060.18341420.15562660X-RAY DIFFRACTION100

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