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- PDB-4z2c: Quinolone(Moxifloxacin)-DNA cleavage complex of gyrase from S. pn... -

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Basic information

Entry
Database: PDB / ID: 4z2c
TitleQuinolone(Moxifloxacin)-DNA cleavage complex of gyrase from S. pneumoniae
Components
  • (DNA gyrase subunit ...) x 2
  • (Symmetrized E-site ...) x 2
KeywordsISOMERASE / Gyrase / Cleavage complex / DNA / quinolone
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling activity / 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
Rossmann fold - #670 / DNA gyrase, subunit A / 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 gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA topoisomerase, type IIA, alpha-helical domain superfamily ...Rossmann fold - #670 / DNA gyrase, subunit A / 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 gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / 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 / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain / 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 gyrase subunit B / DNA gyrase subunit B / DNA gyrase subunit A / DNA gyrase subunit A
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 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 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: 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 A
C: DNA gyrase subunit B
B: DNA gyrase subunit A
D: DNA gyrase subunit B
E: Symmetrized E-site DNA
F: Symmetrized E-site DNA
H: Symmetrized E-site DNA
G: Symmetrized E-site DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,74212
Polymers194,8918
Non-polymers8514
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20370 Å2
ΔGint-152 kcal/mol
Surface area57370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.030, 94.950, 274.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA gyrase subunit ... , 2 types, 4 molecules ABCD

#1: Protein DNA gyrase subunit A /


Mass: 56747.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: gyrA, BM52_0349 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9R867, UniProt: Q8DPM2*PLUS, EC: 5.99.1.3
#2: Protein DNA gyrase subunit B /


Mass: 30286.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: gyrB, BM52_1967, DJ38_04430 / Production host: Escherichia coli (E. coli)
References: UniProt: Q59957, UniProt: P0A4M0*PLUS, EC: 5.99.1.3

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Symmetrized E-site ... , 2 types, 4 molecules EGFH

#3: DNA chain Symmetrized E-site DNA


Mass: 4589.994 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: DNA chain Symmetrized E-site DNA


Mass: 5821.813 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 3 types, 13 molecules

#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 / Moxifloxacin


Mass: 401.431 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H24FN3O4 / Comment: antibiotic*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.91 Å3/Da / Density % sol: 68.59 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 5-10% PEG 8000, 10-20% Ethylene glycol, 0.1M Imidazole/MES buffer system, 0.1M Amino Acids
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: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.03→78.7 Å / Num. obs: 47637 / % possible obs: 99.84 % / Redundancy: 6.49 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 9.6582
Reflection shellResolution: 3.03→3.11 Å / Redundancy: 5.75 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.16 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RAF, 4I3H
Resolution: 3.19→64.245 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 1961 4.8 %Random selection
Rwork0.2233 ---
obs0.2255 40857 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.19→64.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9702 810 60 9 10581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310848
X-RAY DIFFRACTIONf_angle_d0.71714930
X-RAY DIFFRACTIONf_dihedral_angle_d16.4043838
X-RAY DIFFRACTIONf_chiral_restr0.0451745
X-RAY DIFFRACTIONf_plane_restr0.0031824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.19-3.26980.36361430.27782735X-RAY DIFFRACTION100
3.2698-3.35820.37691560.26932688X-RAY DIFFRACTION100
3.3582-3.4570.30641280.25192745X-RAY DIFFRACTION100
3.457-3.56860.35451280.25212772X-RAY DIFFRACTION100
3.5686-3.69610.30091410.23452741X-RAY DIFFRACTION100
3.6961-3.84410.30791520.22252726X-RAY DIFFRACTION100
3.8441-4.0190.23981470.20582734X-RAY DIFFRACTION100
4.019-4.23080.24031290.19522774X-RAY DIFFRACTION100
4.2308-4.49590.24311330.18252770X-RAY DIFFRACTION100
4.4959-4.84290.21951380.18312784X-RAY DIFFRACTION100
4.8429-5.330.25021160.19432813X-RAY DIFFRACTION100
5.33-6.10080.29141590.24732788X-RAY DIFFRACTION100
6.1008-7.68430.25541250.24832874X-RAY DIFFRACTION100
7.6843-64.2580.24641660.23542952X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.7248-6.2073-6.94156.64327.48758.36450.28891.2596-0.1819-0.4008-1.27041.3169-1.0158-0.0241.04940.9270.0786-0.21681.0911-0.11560.790869.6383.5326311.3115
21.9880.52470.23782.01820.54082.21590.0799-0.0913-0.06120.087-0.20210.00360.0566-0.18710.12470.9253-0.0381-0.0940.8124-0.04620.511284.2049-16.3451314.4328
34.3664-0.8494-5.73461.36690.56056.90190.1830.4932-0.3529-0.0789-0.31260.092-0.117-0.83810.28271.0048-0.067-0.11610.7661-0.14390.677578.3755-30.825292.155
48.8042-2.4451-4.22593.8796-1.46454.4277-0.090.87210.1096-0.34640.36050.29170.5865-0.7645-0.25831.1948-0.1759-0.09390.9595-0.15640.634588.2473-30.9865264.0377
59.4846-0.2594-8.63453.31050.3879.47660.0596-1.0474-0.9393-0.4659-0.73820.1916-0.71982.20290.54961.18930.0776-0.28551.2478-0.07560.675982.943-40.714285.2342
67.29736.98097.3177.81797.02427.38010.6540.4209-0.68920.3170.306-0.77371.48310.538-0.96381.2343-0.1268-0.07121.0119-0.0220.777381.8653-35.2735308.4658
79.3328-0.21071.44948.70393.65351.84060.0423-0.23740.13880.1335-0.43750.13550.04710.12480.41911.4235-0.1235-0.04091.12810.16490.544494.9675-12.6021343.8637
80.32110.8909-0.67268.8388-4.48682.478-0.2538-0.82380.67120.4424-0.2114-0.6356-1.70610.29540.43920.9767-0.03280.0481.0609-0.1040.5163124.6696.6089308.4882
92.56820.2825-1.492.6987-0.15772.4450.4946-0.11980.35010.1452-0.10480.1836-1.11270.0401-0.37321.43660.04290.17780.7168-0.01450.6169109.844413.67289.7449
102.50822.80941.00628.22464.74725.2068-0.00540.3727-0.3331-1.01540.3824-1.0504-0.64840.5626-0.24181.34510.01310.17190.93190.01350.6399115.1964-5.3181270.7886
119.29352.02965.50294.7872-3.61578.6753-0.12210.1809-0.0133-0.3925-0.2509-0.5519-0.27480.51210.45861.030.00690.12850.8173-0.09260.7344105.1129-32.1263264.8353
125.58775.6635.16715.78995.21014.7592-0.09131.05660.91670.55040.62020.9589-0.14910.4743-0.58661.53190.17410.07631.12470.0030.8902110.4557-9.7387259.7695
139.0021-8.4099-8.02029.54927.58017.14151.82520.0525-0.0866-2.623-1.2997-0.0937-1.9355-0.1541-0.63241.8559-0.03360.0810.8850.00740.6882111.935812.1866270.1211
148.2929-3.5013-0.90644.4652-3.22864.72140.4525-0.37860.5012-0.3414-0.19460.6746-0.68950.3236-0.27712.5368-0.03220.4360.9449-0.18231.340699.005841.7373299.7371
151.7411-1.09720.18651.76960.26871.28450.1890.03140.4756-0.6375-0.35960.0564-0.8362-0.51020.1511.57990.347-0.121.1109-0.09670.751676.662920.1355312.1423
161.5248-0.42951.32181.543-0.00432.11510.137-0.6275-0.03850.2520.1045-0.2195-0.25950.4318-0.21231.317-0.196-0.09881.253-0.03540.7034117.35943.6145325.0789
177.61353.08292.05438.0772-3.11897.65030.192-2.53330.47381.7624-0.3056-0.5690.48480.28880.03341.4360.2359-0.13711.3863-0.18990.944683.49592.8801325.2873
187.09932.117-3.67892.0718-3.74887.63440.5513-0.90621.881-0.6648-0.28911.2866-2.67320.0989-0.28672.4144-0.1662-0.07631.1413-0.21061.2687109.603417.6391310.3061
192.00052.00461.98543.8373.74793.6663-1.58632.77570.0911.39044.2345-1.81361.97551.6307-2.66681.23930.18730.40161.4617-0.20681.259689.28339.7226316.7521
200.1558-0.31640.17880.6946-0.5821.08240.5250.2755-0.0397-1.4092-0.51040.0129-0.0880.177-0.0342.1693-0.73010.21093.0727-0.70041.103105.587310.5539315.9533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 11:32
2X-RAY DIFFRACTION2chain A and (resseq 33:240 or resseq 325:343 or resseq 478:486)
3X-RAY DIFFRACTION3chain A and resseq 344:386
4X-RAY DIFFRACTION4chain A and resseq 387:432
5X-RAY DIFFRACTION5chain A and resseq 433:457
6X-RAY DIFFRACTION6chain A and resseq 458:477
7X-RAY DIFFRACTION7chain A and resseq 241:324
8X-RAY DIFFRACTION8chain B and resseq 11:32
9X-RAY DIFFRACTION9chain B and (resseq 33:240 or resseq 325:343 or resseq 478:486)
10X-RAY DIFFRACTION10chain B and resseq 344:386
11X-RAY DIFFRACTION11chain B and resseq 387:432
12X-RAY DIFFRACTION12chain B and resseq 433:457
13X-RAY DIFFRACTION13chain B and resseq 458:477
14X-RAY DIFFRACTION14chain B and resseq 241:324
15X-RAY DIFFRACTION15(Chain D and (resseq 401:541 or resseq 585:648)) or (Chain B and resseq 1:10)
16X-RAY DIFFRACTION16(Chain C and (resseq 401:541 or resseq 585:648)) or (Chain A and resseq 1:10)
17X-RAY DIFFRACTION17(Chain E and resseq 7:15) or (Chain F and resseq 1:13)
18X-RAY DIFFRACTION18(Chain G and resseq 9:15) or (Chain H and resseq 1:11)
19X-RAY DIFFRACTION19chain F and resid 101:102
20X-RAY DIFFRACTION20chain H and resid 101:102

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