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- PDB-6qtp: 2.37A structure of gepotidacin with S.aureus DNA gyrase and uncle... -

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Basic information

Entry
Database: PDB / ID: 6qtp
Title2.37A structure of gepotidacin with S.aureus DNA gyrase and uncleaved DNA
Components
  • (DNA gyrase subunit ...) x 2
  • DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*AP*GP*CP*TP*GP*TP*AP*CP*GP*CP*TP*T)-3')
KeywordsISOMERASE / Inhibitor / DNA / Complex
Function / homology
Function and homology information


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 / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
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 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
Similarity search - Domain/homology
Chem-JHN / : / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.37 Å
AuthorsBax, B.D.
CitationJournal: Acs Infect Dis. / Year: 2019
Title: Mechanistic and Structural Basis for the Actions of the Antibacterial Gepotidacin against Staphylococcus aureus Gyrase.
Authors: Gibson, E.G. / Bax, B. / Chan, P.F. / Osheroff, N.
History
DepositionFeb 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_seq_map_depositor_info
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_refine_tls.pdbx_refine_id / _pdbx_refine_tls_group.pdbx_refine_id / _pdbx_seq_map_depositor_info.one_letter_code_mod

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA gyrase subunit B,DNA gyrase subunit B
A: DNA gyrase subunit A
D: DNA gyrase subunit B,DNA gyrase subunit B
C: DNA gyrase subunit A
E: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*AP*GP*CP*TP*GP*TP*AP*CP*GP*CP*TP*T)-3')
F: DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*AP*GP*CP*TP*GP*TP*AP*CP*GP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,35512
Polymers168,5866
Non-polymers7706
Water10,845602
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20900 Å2
ΔGint-138 kcal/mol
Surface area55310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.341, 123.653, 94.099
Angle α, β, γ (deg.)90.00, 117.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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

#1: Protein DNA gyrase subunit B,DNA gyrase subunit B /


Mass: 22605.689 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB, SA0005 / Production host: Escherichia coli (E. coli) / References: UniProt: P66937, EC: 5.99.1.3
#2: Protein DNA gyrase subunit A /


Mass: 55537.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrA, SA0006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99XG5, EC: 5.99.1.3

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DNA chain , 1 types, 2 molecules EF

#3: DNA chain DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*AP*GP*CP*TP*GP*TP*AP*CP*GP*CP*TP*T)-3')


Mass: 6149.978 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 608 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: 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
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-JHN / (3~{R})-3-[[4-(3,4-dihydro-2~{H}-pyrano[2,3-c]pyridin-6-ylmethylamino)piperidin-1-yl]methyl]-1,4,7-triazatricyclo[6.3.1.0^{4,12}]dodeca-6,8(12),9-triene-5,11-dione / Gepotidacin


Mass: 448.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H28N6O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, inhibitor*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 602 / 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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.1
Details: 1ul preciptant solution and 0.7uls complex microbatch under paraffin oil. Precipitant is 9% PEG 5000MME, 80mM BisTris pH 6.1. Complex is 0.055mM dimer of S.aureus B27A56 (=0.11mM monomer), 0. ...Details: 1ul preciptant solution and 0.7uls complex microbatch under paraffin oil. Precipitant is 9% PEG 5000MME, 80mM BisTris pH 6.1. Complex is 0.055mM dimer of S.aureus B27A56 (=0.11mM monomer), 0.16mM duplex DNA (=0.32mM single strand), 60mM Na2SO4, 3mM MnCl2, 18mM Hepes, pH 7.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.584
11H, -K, -H-L20.416
ReflectionResolution: 2.37→50 Å / Num. obs: 66745 / % possible obs: 99 % / Redundancy: 7.3 % / Net I/σ(I): 7.3
Reflection shellResolution: 2.37→2.46 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementResolution: 2.37→49.74 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 8.635 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.049
RfactorNum. reflection% reflectionSelection details
Rfree0.22388 3535 5 %RANDOM
Rwork0.1829 ---
obs0.18503 66745 98.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.26 Å2
Baniso -1Baniso -2Baniso -3
1--23.87 Å20 Å2-2.95 Å2
2--47.77 Å20 Å2
3----23.9 Å2
Refinement stepCycle: 1 / Resolution: 2.37→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10289 785 47 602 11723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01211948
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8111.59816409
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.69851415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.39621.328640
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.338151904
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.88115113
X-RAY DIFFRACTIONr_chiral_restr0.0630.21597
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029009
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9454.5045554
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5856.7496995
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.8614.4176394
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.0684.50354231
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.368→2.43 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 179 -
Rwork0.293 4212 -
obs--82.74 %
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)
11.79360.203-0.55410.9921-0.22721.23520.01640.01850.1523-0.0647-0.0568-0.01930.07590.03360.04040.0710.0112-0.0140.0289-0.04450.12940.060964.03319.7517
20.33350.0413-0.01360.2756-0.02140.3249-0.0204-0.008-0.0502-0.01220.01830.0032-0.0272-0.01010.00210.08780.00650.00120.0034-0.00050.139524.976332.9809-4.0962
32.6782-1.1889-0.55031.0976-0.41890.88680.03920.10480.05850.05470.02690.0293-0.0805-0.1077-0.06610.17140.00190.01010.0328-0.01690.049724.219937.4189-35.7976
42.28180.6555-0.93360.7536-0.15840.6805-0.06210.01530.0529-0.1143-0.06710.00490.025-0.03770.12920.13020.02570.00230.0844-0.00590.085240.48943.3617-48.9589
51.7411-0.0920.53651.56870.58360.4144-0.0126-0.07870.2285-0.0254-0.0272-0.02590.0119-0.04130.03980.089-0.0125-0.02620.0303-0.01520.164220.235858.761714.4172
61.36550.1947-0.05210.69760.0210.37-0.0106-0.071-0.1539-0.01580.01020.0284-0.0244-0.03110.00040.11240.0089-0.00220.01710.04460.150957.337317.557719.4652
70.44650.076-0.08820.44740.03870.259-0.0290.04740.0172-0.04040.0078-0.0066-0.00930.00070.02120.09850.0048-0.01190.01530.01150.11873.006748.868-3.8575
82.4347-0.71782.20092.3710.34652.44960.0690.09450.1182-0.051-0.1018-0.18540.03790.05710.03280.131-0.02050.04260.13970.01540.028473.623745.2863-35.9973
91.57290.44330.13720.69690.79521.02080.03490.19760.0463-0.0070.0318-0.0517-0.0324-0.0203-0.06670.11020.020.0070.07630.0240.046957.223738.2614-48.9859
101.82231.13990.02891.6505-0.8990.9022-0.0309-0.0634-0.2036-0.08490.0167-0.13170.0393-0.05540.01410.12590.0121-0.00110.00690.00580.178477.381222.838914.1965
111.7510.1859-0.10590.340.12991.1476-0.1141-0.1241-0.0258-0.07310.0493-0.02930.10180.13390.06490.08210.01940.02490.03310.00350.10132.715441.692116.4955
120.62060.1629-0.76570.1397-0.11691.12910.0043-0.03880.0134-0.0233-0.01940.0762-0.1246-0.0340.01510.11160.049-0.00770.07290.00720.135665.202140.072716.4208
131.22220.6555-0.02471.45450.051.00840.0728-0.145-0.21810.38060.053-0.17880.1774-0.0351-0.12580.15920.0095-0.04590.06820.06040.127526.096913.973522.6519
140.75180.40940.12130.38170.16830.4050.0872-0.07750.0230.20590.01080.02030.04470.0373-0.09810.20820.0326-0.01550.02910.01120.138971.346368.46523.184
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B417 - 608
2X-RAY DIFFRACTION2A29 - 244
3X-RAY DIFFRACTION2A328 - 369
4X-RAY DIFFRACTION2A461 - 490
5X-RAY DIFFRACTION3A370 - 379
6X-RAY DIFFRACTION3A445 - 460
7X-RAY DIFFRACTION4A380 - 444
8X-RAY DIFFRACTION5A12 - 28
9X-RAY DIFFRACTION5B612 - 637
10X-RAY DIFFRACTION6D417 - 608
11X-RAY DIFFRACTION7C29 - 244
12X-RAY DIFFRACTION7C328 - 369
13X-RAY DIFFRACTION7C461 - 490
14X-RAY DIFFRACTION8C370 - 379
15X-RAY DIFFRACTION8C445 - 460
16X-RAY DIFFRACTION9C380 - 444
17X-RAY DIFFRACTION10C12 - 28
18X-RAY DIFFRACTION10D612 - 637
19X-RAY DIFFRACTION11E2 - 10
20X-RAY DIFFRACTION11F11 - 19
21X-RAY DIFFRACTION12E11 - 19
22X-RAY DIFFRACTION12F2 - 10
23X-RAY DIFFRACTION13A245 - 327
24X-RAY DIFFRACTION14C245 - 327

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