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- PDB-4z3o: Quinolone(Moxifloxacin)-DNA cleavage complex of topoisomerase IV ... -

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Basic information

Entry
Database: PDB / ID: 4z3o
TitleQuinolone(Moxifloxacin)-DNA cleavage complex of topoisomerase IV from S. pneumoniae
Components
  • (E-site DNA) x 4
  • DNA topoisomerase 4 subunit B,ParE30-ParC55 fused topo IV from S. pneumoniae
KeywordsISOMERASE / Topo IV / Cleavage complex / DNA / quinolone
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 / metal ion binding
Similarity search - Function
DNA topoisomerase IV subunit A, Gram-positive / DNA topoisomerase 4 subunit B, Firmicutes/Mollicutes / Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / Rossmann fold - #670 / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / : ...DNA topoisomerase IV subunit A, Gram-positive / DNA topoisomerase 4 subunit B, Firmicutes/Mollicutes / Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / 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 / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA topoisomerase, type IIA, subunit B / 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 / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-MFX / DNA / DNA (> 10) / DNA topoisomerase 4 subunit A / DNA topoisomerase 4 subunit B
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.44 Å
AuthorsLaponogov, I. / Veselkov, D.A. / Pan, X.-S. / Selvarajah, J. / Crevel, I.M.-T. / Fisher, L.M. / Sanderson, M.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/K010069/1 United Kingdom
CitationJournal: To Be Published
Title: Structural studies of the drug-stabilized cleavage complexes of topoisomerase IV and gyrase from Streptococcus pneumoniae
Authors: Laponogov, I. / Veselkov, D.A. / Pan, X.-S. / Selvarajah, J. / Crevel, I.M.-T. / Fisher, L.M. / Sanderson, M.R.
History
DepositionMar 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / struct_conn / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_asym_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.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_conn_type.id
Revision 1.3Oct 23, 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: DNA topoisomerase 4 subunit B,ParE30-ParC55 fused topo IV from S. pneumoniae
B: DNA topoisomerase 4 subunit B,ParE30-ParC55 fused topo IV from S. pneumoniae
E: E-site DNA
F: E-site DNA
G: E-site DNA
H: E-site DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,26412
Polymers179,3646
Non-polymers9006
Water25214
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15210 Å2
ΔGint-112 kcal/mol
Surface area56740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.760, 157.760, 211.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA topoisomerase 4 subunit B,ParE30-ParC55 fused topo IV from S. pneumoniae / Topoisomerase IV subunit B


Mass: 84211.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: parE, SP_0852, Z67739 / Production host: Escherichia coli (E. coli) / References: UniProt: Q59961, UniProt: P72525, EC: 5.99.1.3

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DNA chain , 4 types, 4 molecules EFGH

#2: DNA chain E-site DNA


Mass: 2121.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#3: DNA chain E-site DNA


Mass: 3348.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: DNA chain E-site DNA


Mass: 2113.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#5: DNA chain E-site DNA


Mass: 3358.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 3 types, 20 molecules

#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#7: 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
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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

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Sample preparation

CrystalDensity Matthews: 4.85 Å3/Da / Density % sol: 74.66 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50 mM Na Cacodylate, 100-150 mM NaCl, 4-7% isopropanol
PH range: 6.0-7.0 / Temp details: Incubator

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.17→70.34 Å / Num. obs: 52030 / % possible obs: 99.94 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 5.9986
Reflection shellResolution: 3.17→3.25 Å / Redundancy: 9.76 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 0.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K9F

3k9f


Resolution: 3.44→70.34 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1984 4.86 %Random
Rwork0.1819 ---
obs0.1834 40861 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.44→70.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10247 730 62 14 11053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211308
X-RAY DIFFRACTIONf_angle_d0.63215529
X-RAY DIFFRACTIONf_dihedral_angle_d14.3314110
X-RAY DIFFRACTIONf_chiral_restr0.0421784
X-RAY DIFFRACTIONf_plane_restr0.0021902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4401-3.52610.27751470.23222739X-RAY DIFFRACTION100
3.5261-3.62140.2561460.21522715X-RAY DIFFRACTION100
3.6214-3.7280.24131030.19512781X-RAY DIFFRACTION100
3.728-3.84830.26331410.18982737X-RAY DIFFRACTION100
3.8483-3.98580.25041320.17842755X-RAY DIFFRACTION100
3.9858-4.14540.19831460.17392758X-RAY DIFFRACTION100
4.1454-4.33410.19461470.16082745X-RAY DIFFRACTION100
4.3341-4.56250.19871360.14812755X-RAY DIFFRACTION100
4.5625-4.84830.20521430.15222764X-RAY DIFFRACTION100
4.8483-5.22250.21751220.1672798X-RAY DIFFRACTION100
5.2225-5.74790.23891360.18592799X-RAY DIFFRACTION100
5.7479-6.57910.24991450.2072812X-RAY DIFFRACTION100
6.5791-8.28690.20521670.18452800X-RAY DIFFRACTION100
8.2869-70.35470.17231730.19112919X-RAY DIFFRACTION99
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)
10.153-0.10150.1659.3462-7.08845.42090.10090.0671-0.0113-0.217-0.3926-0.5667-0.23710.63450.16490.5631-0.01510.06520.5015-0.11950.433978.5233-39.6093-9.2058
26.1160.06-0.16518.24411.19598.98580.15750.575-0.2477-0.4117-0.3129-1.30340.18741.00320.14910.30390.01440.02880.57010.10720.500485.3246-61.86528.0424
33.1132-2.21413.13283.34410.67737.80540.2905-2.06561.0152-0.52260.54430.31750.34660.5556-0.6450.9718-0.48590.22961.1056-0.33210.801389.4378-7.1209-4.2192
40.0211-0.00720.06562.2901-1.33080.9123-0.2657-0.4832-0.8249-0.3649-0.5725-1.31860.12830.96610.79230.4212-0.56530.87221.6903-0.34011.2089105.97511.2576-0.7664
52.5152-0.8899-0.1334.09251.55173.8348-0.0165-0.32060.21040.26810.12570.0996-0.19510.0705-0.09860.8357-0.07160.07060.56140.00070.436373.2402-15.8633.8921
62.98231.7053-0.1915.8708-5.65257.86090.0518-0.48980.1016-0.51810.49640.34530.8585-0.4035-0.2240.72310.1760.09220.6943-0.1220.46672.7574-51.669-9.1939
75.011-1.921-0.10065.75671.72642.2443-0.2292-0.2460.05650.15550.23260.813-0.878-0.408-0.03591.16580.2860.02420.60.16490.663353.307112.5044-8.6404
85.6259-5.0312-1.6059.6012.07081.9664-0.1526-0.4581-0.11990.15260.16390.05950.2363-0.04790.01090.6917-0.14710.03120.4215-0.01920.281964.7394-24.5084-16.9412
92.9199-0.8456-0.25462.4084-1.42732.96920.12970.11570.433-0.26530.11690.0559-0.59510.2323-0.26280.9193-0.19040.14730.459-0.0510.480771.7335-9.5403-18.4798
10-0.04950.1652-0.14073.56312.27452.01760.14950.2845-0.0869-0.0471-0.11510.0796-0.1889-0.36610.09730.34140.0079-0.06890.61940.13350.363677.2052-41.814940.9054
114.7775-0.1008-1.20477.9653-0.94267.70090.0657-0.2646-0.0932-0.31780.17870.58490.6272-0.6173-0.16490.3255-0.1309-0.05930.54810.02120.298274.103-63.8121.5636
126.6040.87065.22252.07731.71734.6720.24581.35780.42310.02670.4437-0.6382-0.4157-1.0884-0.50760.70020.03370.21111.02630.38140.673163.7358-9.498838.5607
131.0471.04820.58371.02760.59950.33540.4585-0.2965-1.07840.93060.05581.2192-0.0654-0.9885-0.21950.41130.05170.0571.04990.36731.174746.9966-2.348236.2684
143.27791.1303-0.06755.2659-0.11324.7934-0.1090.09720.187-0.47910.2580.15790.3943-0.1439-0.11560.6041-0.0633-0.0550.45930.07320.331580.2619-16.712829.625
155.1301-3.1644-1.64835.11596.23789.20380.11610.03780.11860.4910.6767-0.80930.12690.3491-0.59370.7741-0.14680.02350.47720.13030.454484.1371-52.704339.8568
167.93031.60860.86177.1542-0.96484.47210.22680.24840.0846-0.1977-0.0317-0.593-0.27470.5143-0.160.6569-0.1336-0.0050.4693-0.1470.51499.344311.195244.3678
172.92022.3998-0.19026.3012-1.75530.89120.0482-0.15290.07610.1399-0.163-0.41340.36710.02890.13910.71930.1066-0.01130.57250.01720.282189.4239-26.134749.4007
181.9661-0.1335-0.29113.10090.51451.25010.1254-0.44810.13590.61520.1587-0.1142-0.0216-0.0781-0.30120.76720.0128-0.01480.5550.0360.354381.5519-12.286552.3301
191.04770.2070.79966.1012-5.88159.4134-0.67630.0276-1.84-0.76810.87340.00321.04881.316-0.15190.53610.00430.19361.0209-0.32581.1786104.4264-15.102212.2941
206.30890.0726-2.2186.4673-1.99232.6188-0.39810.88971.1233-1.00650.79-0.3703-0.59910.6728-0.32631.3185-0.61320.39031.5351-0.06361.036697.62385.7569-11.7209
213.2112-0.35680.0037-0.0696-0.33351.4107-0.6018-0.17110.6386-0.23510.4395-0.4775-0.46160.52640.17791.2015-0.51090.05761.2391-0.27611.1038100.50467.744110.8198
220.3084-1.3767-0.98366.87285.80825.7985-0.02831.3223-0.0512-0.20510.71591.2374-0.3709-0.0433-0.60190.5893-0.071-0.05090.90010.02981.223849.2607-17.075120.8123
231.4774-0.80230.60991.38060.62311.17090.3655-0.58110.5480.6641-0.30241.3036-0.5916-1.0540.04781.12380.50620.30731.29550.29281.264254.35182.225946.8381
242.21091.1220.00591.4080.07891.391-0.37140.2380.5675-0.20550.420.9305-0.4934-0.2722-0.00790.83470.313-0.01321.04580.3441.125951.92515.837524.8089
258.7071-0.6107-0.56288.0987-2.78981.01330.2592-0.28481.0329-0.6760.7468-0.3602-1.37230.7039-1.04651.28670.00580.2831.2081-0.13850.754273.81573.47533.5981
262.4701-0.1959-1.76986.84494.0683.59680.1953-0.44290.92330.7950.51320.5151-1.3722-0.2803-0.80231.7336-0.22410.16861.24030.0380.877778.35984.89891.7466
275.35222.4837-1.37376.1251-2.00440.7280.55590.3294-0.35140.3662-2.2568-1.31310.7988-0.8161.45061.6092-0.1470.46681.15340.19570.921581.60474.559511.1827
287.7344-2.85120.48431.34660.66522.43750.3673-0.0436-0.30690.0499-0.3829-0.01211.05630.25080.11131.16990.12180.38711.0587-0.0080.661470.4853.746524.0856
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain "A" and resseq 1343:1382
2X-RAY DIFFRACTION2chain "A" and resseq 1383:1429
3X-RAY DIFFRACTION3chain "A" and resseq 1018:1030
4X-RAY DIFFRACTION4chain "A" and resseq 1002:1017
5X-RAY DIFFRACTION5chain "A" and resseq 1031:1154
6X-RAY DIFFRACTION6chain "A" and resseq 1430:1455
7X-RAY DIFFRACTION7chain "A" and resseq 1239:1322
8X-RAY DIFFRACTION8chain "A" and resseq 1456:1482
9X-RAY DIFFRACTION9chain "A" and (resseq 1155:1238 or resseq 1323:1342)
10X-RAY DIFFRACTION10chain "B" and resseq 1343:1382
11X-RAY DIFFRACTION11chain "B" and resseq 1383:1429
12X-RAY DIFFRACTION12chain "B" and resseq 1018:1030
13X-RAY DIFFRACTION13chain "B" and resseq 1002:1017
14X-RAY DIFFRACTION14chain "B" and resseq 1031:1154
15X-RAY DIFFRACTION15chain "B" and resseq 1430:1455
16X-RAY DIFFRACTION16chain "B" and resseq 1239:1322
17X-RAY DIFFRACTION17chain "B" and resseq 1456:1482
18X-RAY DIFFRACTION18chain "B" and (resseq 1155:1238 or resseq 1323:1342)
19X-RAY DIFFRACTION19chain "A" and resseq 539:581
20X-RAY DIFFRACTION20chain "A" and resseq 610:634
21X-RAY DIFFRACTION21chain "A" and (resseq 415:538 or resseq 582:609 or resseq 635:640 or resid 742)
22X-RAY DIFFRACTION22chain "B" and resseq 539:581
23X-RAY DIFFRACTION23chain "B" and resseq 610:634
24X-RAY DIFFRACTION24chain "B" and (resseq 415:538 or resseq 582:609 or resseq 635:640 or resid 742)
25X-RAY DIFFRACTION25(chain "E" or chain "F" ) and resseq 1:20
26X-RAY DIFFRACTION26(chain "G" or chain "H" ) and resseq 1:20
27X-RAY DIFFRACTION27(chain "E" or chain "F" ) and resseq 101:102
28X-RAY DIFFRACTION28(chain "G" or chain "H" ) and resseq 101:102

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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