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- PDB-2xkk: CRYSTAL STRUCTURE OF MOXIFLOXACIN, DNA, and A. BAUMANNII TOPO IV ... -

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Basic information

Entry
Database: PDB / ID: 2xkk
TitleCRYSTAL STRUCTURE OF MOXIFLOXACIN, DNA, and A. BAUMANNII TOPO IV (PARE-PARC FUSION TRUNCATE)
Components
  • (DNA) x 2
  • TOPOISOMERASE IV
KeywordsISOMERASE/DNA/ANTIBIOTIC / ISOMERASE-DNA-ANTIBIOTIC COMPLEX / TYPE IIA TOPOISOMERASE / QUINOLONE / ANTIBACTERIAL AGENT
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling 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 gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, alpha-helical domain superfamily ...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 gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / 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 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
Chem-MFX / DNA / DNA (> 10) / DNA topoisomerase 4 subunit B / DNA topoisomerase 4 subunit A
Similarity search - Component
Biological speciesACINETOBACTER BAUMANNII (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 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 1.1Oct 12, 2011Group: Database references / Version format compliance
Revision 1.2Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TOPOISOMERASE IV
C: TOPOISOMERASE IV
E: DNA
F: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,14710
Polymers193,2474
Non-polymers9006
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16180 Å2
ΔGint-102.1 kcal/mol
Surface area62960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)199.775, 95.566, 118.092
Angle α, β, γ (deg.)90.00, 108.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein TOPOISOMERASE IV


Mass: 86165.758 Da / Num. of mol.: 2
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 / Plasmid: PET22B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B0V9T6, UniProt: B0VP98, Isomerases; Other isomerases; Sole sub-subclass for isomerases that do not belong in the other subclasses

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DNA chain , 2 types, 2 molecules EF

#2: DNA chain DNA


Mass: 10493.806 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA CLEAVED INTO 2, COMPLEX TRAPPED BY MFX / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain DNA


Mass: 10421.695 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA CLEAVED INTO 2, COMPLEX TRAPPED BY MFX / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 3 types, 46 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-MFX / 1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid / moxifloxacin


Mass: 401.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24FN3O4 / Comment: antibiotic*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.63 Å3/Da / Density % sol: 53.18 % / Description: NONE
Crystal growDetails: 8% PEG 5000MME, 200 MM TRIS PH 8.5, 100 MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 3.27→36 Å / Num. obs: 32221 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 109 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.7
Reflection shellResolution: 3.27→3.33 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.3 / % possible all: 98.5

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Processing

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

2xkj


Resolution: 3.25→36.17 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 29.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.27 1316 4.1 %
Rwork0.194 --
obs0.197 32221 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 96.77 Å2 / ksol: 0.29 e/Å3
Displacement parametersBiso mean: 133.6 Å2
Baniso -1Baniso -2Baniso -3
1--29.2545 Å20 Å2-17.9842 Å2
2--18.7098 Å20 Å2
3---10.5447 Å2
Refinement stepCycle: LAST / Resolution: 3.25→36.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10691 1058 62 40 11851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01312185
X-RAY DIFFRACTIONf_angle_d1.49316775
X-RAY DIFFRACTIONf_dihedral_angle_d19.4354548
X-RAY DIFFRACTIONf_chiral_restr0.0741942
X-RAY DIFFRACTIONf_plane_restr0.0052002
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2554-3.38570.34441410.26583264X-RAY DIFFRACTION93
3.3857-3.53970.30591570.24433498X-RAY DIFFRACTION99
3.5397-3.72610.35631580.23033467X-RAY DIFFRACTION99
3.7261-3.95930.27581370.19783515X-RAY DIFFRACTION99
3.9593-4.26450.2531360.17823329X-RAY DIFFRACTION94
4.2645-4.69290.24641220.15523529X-RAY DIFFRACTION99
4.6929-5.37010.22131450.15373536X-RAY DIFFRACTION99
5.3701-6.75850.27431670.18363501X-RAY DIFFRACTION99
6.7585-36.16780.24181530.18663266X-RAY DIFFRACTION90
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1184-0.6231-0.9530.3513-0.35051.8057-0.23840.34470.9872-0.20740.0718-0.2792-0.81040.7256-0.00011.7952-0.3526-0.2160.9982-0.05852.1077-16.214164.2109-17.8156
20.0742-0.0065-0.04020.1033-0.0820.05610.77410.7043-0.0648-0.1627-0.90991.7363-0.7513-0.18850.00022.2738-0.1615-0.45121.69240.23082.5535-41.006967.7118-28.6754
30.166-0.0343-0.23250.14770.21110.22490.4951-0.55971.14150.1886-0.5320.0676-0.18190.34130.00061.9867-0.0823-0.08111.228-0.52661.9101-26.86166.31-0.0976
43.478-0.3269-1.20560.48240.51943.7261-0.224-0.66370.73160.1536-0.0189-0.0746-0.4835-0.2942-00.95470.1698-0.0390.7305-0.39030.8357-43.852838.9538-1.2371
50.6373-0.5588-0.50620.47290.40660.82630.022-1.0265-0.32790.2113-0.3497-0.23480.32040.39430.00041.10190.097-0.00021.59350.05821.056-19.374420.782712.3293
60.08140.07910.09340.04020.05890.0935-0.5197-0.8185-0.1744-0.45690.50790.3099-0.3583-1.06680.00011.17040.2740.00171.3636-0.28041.6026-75.022340.535-12.0109
70.4498-0.0887-0.03560.2510.43410.91130.02230.03120.0332-0.4561-0.22771.12670.0563-0.72350.00061.24180.0976-0.171.4477-0.00591.4507-83.857843.4856-32.678
80.1620.0519-0.04650.08150.03410.2063-0.25060.6930.05520.3254-0.22190.0039-0.27850.623-0.00081.2518-0.2033-0.2481.69120.29631.0692-61.241334.5442-56.501
90.7669-0.04990.14880.26220.44870.9967-0.55780.62910.2206-0.58090.41051.1243-0.0223-1.1906-0.00011.176-0.1249-0.24351.47250.07381.3949-80.08130.7741-44.8506
102.1383-0.65240.7610.2836-0.69680.7544-0.4521-0.17210.71580.24240.0525-0.703-0.27070.7406-0.00011.1763-0.2853-0.10391.25610.0331.4212-13.485538.1383-19.3872
112.22630.78391.04052.15170.69423.6782-0.0169-0.214-0.1342-0.02160.0158-0.2540.28940.26480.00010.92020.01710.12410.87750.13050.9405-15.005612.9001-19.3375
120.1736-0.08740.24160.0624-0.20950.34730.2341-0.48720.2119-0.40870.21410.7740.903-1.19270.00121.2692-0.2073-0.11421.35650.13831.5547-41.28869.2443-24.711
130.2292-0.2364-0.10540.68140.52890.50570.1910.8937-0.7211-0.6-0.61970.2316-0.0288-0.1596-0.00061.0173-0.16440.28330.9960.04920.9204-13.855611.0979-40.2908
142.9245-0.0088-0.38790.4501-0.16393.5553-0.07380.89630.481-0.29660.0366-0.0686-0.3220.05250.00031.0537-0.1790.0011.07110.32420.8412-29.386437.4957-48.5872
150.17270.44470.0620.39530.21950.30750.2142-0.01370.6069-0.2937-0.2664-0.7801-0.33910.3315-01.6262-0.54190.13691.62810.58172.0021-2.065856.8288-46.6072
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1((CHAIN A AND (RESID 385:503 OR RESID 539:567)))
2X-RAY DIFFRACTION2((CHAIN A AND (RESID 504:538)))
3X-RAY DIFFRACTION3((CHAIN A AND (RESID 569:596)) OR ((CHAIN A) AND (RESID 1013:1026)))
4X-RAY DIFFRACTION4((CHAIN A AND (RESID 1027:1246 OR RESID 1326:1367 OR RESID 1457:1486)))
5X-RAY DIFFRACTION5((CHAIN A AND (RESID 1247:1325)))
6X-RAY DIFFRACTION6((CHAIN A AND (RESID 1368:1378)) OR (CHAIN A AND (RESID 1439:1455)))
7X-RAY DIFFRACTION7((CHAIN A AND (RESID 1379:1434)))
8X-RAY DIFFRACTION8((CHAIN C AND (RESID 1368:1378)) OR (CHAIN C AND (RESID 1439:1455)))
9X-RAY DIFFRACTION9((CHAIN C AND (RESID 1379:1434)))
10X-RAY DIFFRACTION10((CHAIN E) OR (CHAIN F))
11X-RAY DIFFRACTION11((CHAIN C AND (RESID 385:503 OR RESID 539:567)))
12X-RAY DIFFRACTION12((CHAIN C AND (RESID 504:538)))
13X-RAY DIFFRACTION13((CHAIN C AND (RESID 569:596)) OR ((CHAIN C) AND (RESID 1013:1026)))
14X-RAY DIFFRACTION14((CHAIN C AND (RESID 1027:1246 OR RESID 1326:1367 OR RESID 1457:1486)))
15X-RAY DIFFRACTION15((CHAIN C AND (RESID 1247:1325)))

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