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- PDB-4juo: A low-resolution three-gate structure of topoisomerase IV from St... -

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Basic information

Entry
Database: PDB / ID: 4juo
TitleA low-resolution three-gate structure of topoisomerase IV from Streptococcus pneumoniae in space group H32
Components
  • (DNA topoisomerase 4 subunit ...) x 2
  • (E-site DNA) x 4
KeywordsISOMERASE/DNA / full-length ParE / ParC55 / open N-gate / topoisomerase IIa / ATP binding / ISOMERASE-DNA complex
Function / homology
Function and homology information


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 / metal ion binding / cytoplasm
Similarity search - Function
DNA topoisomerase IV subunit A, Gram-positive / DNA topoisomerase 4 subunit B, Firmicutes/Mollicutes / 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, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / Topoisomerase (Topo) IIA-type catalytic domain profile. ...DNA topoisomerase IV subunit A, Gram-positive / DNA topoisomerase 4 subunit B, Firmicutes/Mollicutes / 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, subunit B / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / Topoisomerase (Topo) IIA-type catalytic domain profile. / 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 superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
Chem-LFX / DNA / DNA (> 10) / DNA topoisomerase 4 subunit A / DNA topoisomerase 4 subunit B
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
Streptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.53 Å
AuthorsLaponogov, I. / Veselkov, D.A. / Pan, X.-S. / Crevel, I. / Fisher, L.M. / Sanderson, M.R.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structure of an 'open' clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport.
Authors: Laponogov, I. / Veselkov, D.A. / Crevel, I.M. / Pan, X.S. / Fisher, L.M. / Sanderson, M.R.
History
DepositionMar 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Dec 4, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase 4 subunit A
C: DNA topoisomerase 4 subunit B
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)147,2769
Polymers146,8666
Non-polymers4103
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)213.580, 213.580, 211.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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DNA topoisomerase 4 subunit ... , 2 types, 2 molecules AC

#1: Protein DNA topoisomerase 4 subunit A / Topoisomerase IV subunit A


Mass: 56455.434 Da / Num. of mol.: 1 / Fragment: ParC55
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: ATCC BAA-334 / TIGR4 / Gene: parC, SP_0855 / Production host: Escherichia coli (E. coli) / References: UniProt: P72525, EC: 5.99.1.3
#2: Protein DNA topoisomerase 4 subunit B


Mass: 74528.180 Da / Num. of mol.: 1 / Fragment: ParE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: parE / Production host: Escherichia coli (E. coli) / References: UniProt: Q59961, EC: 5.99.1.3

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DNA chain , 4 types, 4 molecules EFGH

#3: DNA chain E-site DNA


Mass: 3397.247 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: DNA chain E-site DNA


Mass: 4543.972 Da / Num. of mol.: 1 / Source method: obtained synthetically
#5: DNA chain E-site DNA


Mass: 3339.195 Da / Num. of mol.: 1 / Source method: obtained synthetically
#6: DNA chain E-site DNA


Mass: 4602.025 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 2 types, 3 molecules

#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-LFX / (3S)-9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid / Levofloxacin


Mass: 361.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20FN3O4

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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: 3.17 Å3/Da / Density % sol: 61.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 3-4% isopropanol, 50 mM Na cacodylate, optimised mixture of salts, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 26, 2010
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 6.53→53.4 Å / Num. all: 3718 / Num. obs: 3701 / % possible obs: 99.24 % / Observed criterion σ(F): -1 / Observed criterion σ(I): -1 / Redundancy: 9.66 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.84
Reflection shellResolution: 6.53→6.71 Å / Redundancy: 10.93 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.88 / Num. unique all: 309 / % possible all: 99.66

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Processing

Software
NameVersionClassification
GDEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
xia2data reduction
XDSdata reduction
xia2data scaling
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RAE

3rae


Resolution: 6.53→46.442 Å / SU ML: 0.88 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 40.82 / Stereochemistry target values: ML
Details: Refinement has been limited to rigid body and TLS refinement only due to the low resolution
RfactorNum. reflection% reflectionSelection details
Rfree0.2982 169 4.57 %Random
Rwork0.2474 ---
obs0.2498 3701 99.14 %-
all-3718 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 6.53→46.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7498 730 28 0 8256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0178469
X-RAY DIFFRACTIONf_angle_d1.49111661
X-RAY DIFFRACTIONf_dihedral_angle_d18.673005
X-RAY DIFFRACTIONf_chiral_restr0.0841362
X-RAY DIFFRACTIONf_plane_restr0.0071394
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)
1-0.0023-0.04630.0208-0.0519-0.1301-0.03580.4113-0.66860.75610.4411-0.09750.53480.75510.06700.6393-0.6341-0.80260.2886-0.1916-0.101542.8117-24.308389.8941
20.00960.0119-0.0472-0.0218-0.0457-0.0484-0.468-0.20030.8468-0.2569-0.36010.7366-0.0377-0.2719-0-2.52611.37353.62950.8302-0.898-1.177652.2602-39.495277.0999
3-0.0282-0.00960.0094-0.0073-0.02230.0201-0.1178-0.05080.1895-0.21680.07550.1773-0.09580.2323-0-0.1094-0.9205-0.40840.8212-0.66140.305262.0692-34.465384.6278
40.0158-0.0268-0.0189-0.0082-0.03180.04680.0422-0.2756-0.26710.3956-0.08720.28440.1640.0196-0-0.16410.08230.38750.23120.20140.770662.2868-36.944780.797
50.03570.0335-0.0194-0.03940.01970.04570.18060.15590.29910.5203-0.33790.10050.1186-0.0117-00.2855-0.58611.1710.8738-0.0395-0.129347.0923-36.682492.4337
60.0254-0.02580.0350.06910.0470.049-0.011-0.01920.18540.0805-0.2822-0.26440.0260.220402.8074-0.3646-1.1170.7211-1.66040.022959.153-41.377110.5963
7-0.01050.0082-0.0957-0.0438-0.01060.0484-0.67780.14310.31540.6143-1.4766-1.077-0.22590.8694-01.0068-1.4799-0.01091.8047-1.6065-0.362876.3203-25.7235101.5645
80.03650.0152-0.00760.0040.03730.0148-0.3689-0.10810.64840.1984-0.252-0.1726-0.6429-0.340300.2983-0.54830.35581.4388-0.68761.482888.0322-23.385793.2793
9-0.003-0.0159-0.03210.1020.0454-0.0305-0.1260.09270.1232-0.0317-0.3185-0.4366-0.2024-0.235201.2842-0.3331-0.52280.7079-0.04461.997364.9824-23.1283103.4675
10-0.00450.1795-0.2176-0.15810.1679-0.0035-0.20670.06390.1349-0.09330.46150.08081.0899-0.8270-0.89-2.30041.8643-0.22692.5144-2.661333.267-61.008691.9895
110.0841-0.31830.13240.45960.2633-0.4027-0.6196-1.1727-0.0055-0.0882-0.62430.10171.14711.7466-01.1728-0.89620.0541-1.609-1.3857-0.152838.0794-62.730791.5056
120.13690.0757-0.0936-0.0545-0.0430.0690.2621-0.07770.4661-0.58010.1748-0.02440.22270.1219-03.60220.94820.17132.7473-0.1781.523517.544817.444422.405
130.1220.17780.15030.23550.309-0.1331.08560.7790.11830.1249-0.05530.45590.0849-1.114401.1619-2.15390.9383-3.86550.85650.904433.724320.329253.7648
140.01050.4021-0.07040.05160.0504-0.0191-0.2241-0.81271.2714-0.0820.65960.52840.7642-0.86601.23140.302-0.1920.42690.22620.914638.6977-6.449481.1903
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 50 )
2X-RAY DIFFRACTION2chain 'A' and (resid 51 through 77 )
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 107 )
4X-RAY DIFFRACTION4chain 'A' and (resid 108 through 131 )
5X-RAY DIFFRACTION5chain 'A' and (resid 132 through 182 )
6X-RAY DIFFRACTION6chain 'A' and (resid 183 through 217 )
7X-RAY DIFFRACTION7chain 'A' and (resid 218 through 277 )
8X-RAY DIFFRACTION8chain 'A' and (resid 278 through 307 )
9X-RAY DIFFRACTION9chain 'A' and (resid 308 through 342 )
10X-RAY DIFFRACTION10chain 'A' and (resid 343 through 394 )
11X-RAY DIFFRACTION11chain 'A' and (resid 395 through 484 )
12X-RAY DIFFRACTION12chain 'C' and (resid 24 through 203 )
13X-RAY DIFFRACTION13chain 'C' and (resid 204 through 444 )
14X-RAY DIFFRACTION14chain 'C' and (resid 445 through 640 )

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