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- PDB-5cdp: 2.45A structure of etoposide with S.aureus DNA gyrase and DNA -

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Basic information

Entry
Database: PDB / ID: 5cdp
Title2.45A structure of etoposide with S.aureus DNA gyrase and DNA
Components
  • (DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*G*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)- ...) x 2
  • (DNA gyrase subunit ...) x 2
KeywordsISOMERASE / TYPE IIA TOPOISOMERASE / ANTIBACTERIAL / INHIBITOR / fusion protein
Function / homology
Function and homology information


DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA negative supercoiling 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
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 / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA gyrase B subunit, C-terminal ...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 / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EVP / : / 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 / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsBax, B.D. / Srikannathasan, V. / Chan, P.F.
Citation
Journal: Nat Commun / Year: 2015
Title: Structural basis of DNA gyrase inhibition by antibacterial QPT-1, anticancer drug etoposide and moxifloxacin.
Authors: Chan, P.F. / Srikannathasan, V. / Huang, J. / Cui, H. / Fosberry, A.P. / Gu, M. / Hann, M.M. / Hibbs, M. / Homes, P. / Ingraham, K. / Pizzollo, J. / Shen, C. / Shillings, A.J. / Spitzfaden, ...Authors: Chan, P.F. / Srikannathasan, V. / Huang, J. / Cui, H. / Fosberry, A.P. / Gu, M. / Hann, M.M. / Hibbs, M. / Homes, P. / Ingraham, K. / Pizzollo, J. / Shen, C. / Shillings, A.J. / Spitzfaden, C.E. / Tanner, R. / Theobald, A.J. / Stavenger, R.A. / Bax, B.D. / Gwynn, M.N.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Crystallization and initial crystallographic analysis of covalent DNA-cleavage complexes of Staphyloccocus aureus DNA gyrase with QPT-1, moxifloxacin and etoposide.
Authors: Srikannathasan, V. / Wohlkonig, A. / Shillings, A. / Singh, O. / Chan, P.F. / Huang, J. / Gwynn, M.N. / Fosberry, A.P. / Homes, P. / Hibbs, M. / Theobald, A.J. / Spitzfaden, C. / Bax, B.D.
History
DepositionJul 4, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_alt_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_alt_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_alt_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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)165,80514
Polymers165,0068
Non-polymers7996
Water13,818767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22220 Å2
ΔGint-141 kcal/mol
Surface area57170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.364, 93.364, 411.244
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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

#1: Protein DNA gyrase subunit A


Mass: 54738.453 Da / Num. of mol.: 2 / Fragment: UNP residues 9-491
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria)
Strain: N315 / Gene: gyrA, SA0006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99XG5, EC: 5.99.1.3
#2: Protein DNA gyrase subunit B / Greek key deletion construct


Mass: 21345.270 Da / Num. of mol.: 2 / Fragment: UNP residues 417-542, 580-640
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain N315) (bacteria)
Strain: N315 / Gene: gyrB, SA0005 / Production host: Escherichia coli (E. coli) / References: UniProt: P66937, EC: 5.99.1.3

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DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*G*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)- ... , 2 types, 4 molecules EFGH

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


Mass: 2451.630 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*G*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3')


Mass: 3967.585 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 773 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-EVP / (5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol -5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside / Etoposide / VP-16


Mass: 588.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H32O13
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 767 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailschains B and D is a Greek key deletion construct in which residues 544-579 of GyrB have been ...chains B and D is a Greek key deletion construct in which residues 544-579 of GyrB have been deleted and replaced with two residues TG.

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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: 3.13 Å3/Da / Density % sol: 60.75 %
Crystal growTemperature: 293 K / Method: microbatch / Details: 150mM Bistris pH6.2, 11% PEG 5000 MME / PH range: 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.45→40 Å / Num. obs: 70926 / % possible obs: 95.9 % / Redundancy: 2.8 % / Biso Wilson estimate: 46.32 Å2 / Rmerge(I) obs: 0.084 / Χ2: 1.026 / Net I/av σ(I): 12.224 / Net I/σ(I): 8.2 / Num. measured all: 199618
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.45-2.492.80.44834950.95895.5
2.49-2.542.90.40335190.95795.9
2.54-2.592.80.35235440.98695.5
2.59-2.642.90.31535090.99495.7
2.64-2.72.80.27335551.00996.1
2.7-2.762.80.2435440.96495.7
2.76-2.832.80.20235991.00196.3
2.83-2.92.80.17935290.99696
2.9-2.992.80.14635080.99295.7
2.99-3.092.80.13135611.00496.1
3.09-3.22.80.11135471.02996.3
3.2-3.322.80.09135671.00696.1
3.32-3.482.80.07635421.04495.6
3.48-3.662.80.06335230.97795.7
3.66-3.892.80.05835611.02495.9
3.89-4.192.70.05735321.14195.8
4.19-4.612.80.06535611.64195.9
4.61-5.272.80.06235481.5496
5.27-6.642.70.04535940.83496.2
6.64-402.80.02135880.45795.5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.11.5refinement
PDB_EXTRACT3.15data extraction
PHENIXphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XCS

2xcs


Resolution: 2.45→39.78 Å / Cor.coef. Fo:Fc: 0.9395 / Cor.coef. Fo:Fc free: 0.9154 / SU R Cruickshank DPI: 0.345 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.347 / SU Rfree Blow DPI: 0.218 / SU Rfree Cruickshank DPI: 0.221
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2860 4.03 %RANDOM
Rwork0.1766 ---
obs0.178 70923 95.88 %-
Displacement parametersBiso max: 131.28 Å2 / Biso mean: 37.83 Å2 / Biso min: 3.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.9203 Å20 Å20 Å2
2--0.9203 Å20 Å2
3----1.8407 Å2
Refine analyzeLuzzati coordinate error obs: 0.283 Å
Refinement stepCycle: final / Resolution: 2.45→39.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10611 801 48 770 12230
Biso mean--46.57 38.79 -
Num. residues----1385
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4397SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes335HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1700HARMONIC5
X-RAY DIFFRACTIONt_it12151HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1594SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14423SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12151HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg16614HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion17.37
LS refinement shellResolution: 2.45→2.51 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2491 178 3.48 %
Rwork0.2181 4932 -
all0.2192 5110 -
obs--95.88 %
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)
13.20510.248-1.02240.4943-0.38260.69270.013-0.34110.2569-0.0010.01260.1253-0.03230.0476-0.02560.09160.01390.01490.0452-0.0920.027613.567154.139163.5699
21.00360.1172-0.01441.003-0.00360.845-0.0077-0.0128-0.13330.08920.0093-0.01780.0350.0281-0.0016-0.02520.01160.0199-0.1168-0.0147-0.036730.154529.447634.4189
3-1.35161.1690.84372.4014-0.65250.5606-0.00080.0571-0.0003-0.0107-0.0445-0.06790.02150.09610.04530.10590.03970.0051-0.0737-0.00330.125629.7393-2.151740.6425
43.74840.7670.63431.630.11330.00050.112-0.1881-0.061-0.032-0.0445-0.21550.088-0.1848-0.06740.13530.03130.0109-0.05370.01290.05411.4855-13.327246.3929
52.9039-0.09020.76580.83062.38744.4554-0.0011-0.30040.05830.1801-0.0176-0.08740.11450.10260.01870.0770.033-0.00030.0796-0.00420.004632.966647.011861.8178
64.4306-0.8232-0.57831.41060.51590.6911-0.00370.370.3353-0.07340.0344-0.12-0.2424-0.0363-0.03070.16930.04980.02140.12530.0850.0673-0.480753.77916.5289
71.0923-0.0406-0.0590.55510.06440.6315-0.0242-0.0134-0.16-0.0493-0.0280.01270.01220.01380.05220.01290.0650.02-0.0883-0.0213-0.0252-18.638834.184348.0776
8-0.0022-0.55181.35872.0690.06620.68550.0434-0.02570.0314-0.0152-0.06510.08410.0502-0.03820.02170.0668-0.01180.0325-0.0712-0.06350.1655-22.9212.437343.8096
93.5642-0.5585-0.02251.4889-0.07690.29980.0439-0.0972-0.1630.0023-0.04810.0320.05420.09680.00410.09440.02610.0143-0.1042-0.03940.0402-7.3218-11.724440.7547
103.1185-0.45961.80840.9928-0.96123.8957-0.01250.29740.0284-0.1661-0.0072-0.00280.029-0.16340.01970.15520.086-0.0120.13490.0016-0.0166-20.821949.819418.7056
110.9631-0.7961-0.2890.26040.36791.4662-0.05030.13880.1285-0.18560.00740.1239-0.2016-0.23860.04290.0634-0.0441-0.0267-0.00350.03380.156319.959850.947840.378
121.68890.9277-0.57330.8307-0.47741.0586-0.0461-0.08090.15750.14590.0163-0.0702-0.1380.17710.02990.14450.1406-0.02990.0245-0.03610.1576-10.703953.640639.6435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|417 - B|608 M|1001 }B417 - 608
2X-RAY DIFFRACTION1{ B|417 - B|608 M|1001 }M1001
3X-RAY DIFFRACTION2{ A|29 - A|244 A|328 - A|369 A|461 - A|491 }A29 - 244
4X-RAY DIFFRACTION2{ A|29 - A|244 A|328 - A|369 A|461 - A|491 }A328 - 369
5X-RAY DIFFRACTION2{ A|29 - A|244 A|328 - A|369 A|461 - A|491 }A461 - 491
6X-RAY DIFFRACTION3{ A|374 - A|379 A|451 - A|460 }A374 - 379
7X-RAY DIFFRACTION3{ A|374 - A|379 A|451 - A|460 }A451 - 460
8X-RAY DIFFRACTION4{ A|380 - A|450 }A380 - 450
9X-RAY DIFFRACTION5{ A|9 - A|28 B|609 - B|640 }A9 - 28
10X-RAY DIFFRACTION5{ A|9 - A|28 B|609 - B|640 }B609 - 640
11X-RAY DIFFRACTION6{ D|417 - D|608 M|1 }D417 - 608
12X-RAY DIFFRACTION6{ D|417 - D|608 M|1 }M1
13X-RAY DIFFRACTION7{ C|29 - C|244 C|328 - C|329 C|461 - C|490 }C29 - 244
14X-RAY DIFFRACTION7{ C|29 - C|244 C|328 - C|329 C|461 - C|490 }C328 - 329
15X-RAY DIFFRACTION7{ C|29 - C|244 C|328 - C|329 C|461 - C|490 }C461 - 490
16X-RAY DIFFRACTION8{ C|373 - C|379 C|451 - C|460 }C373 - 379
17X-RAY DIFFRACTION8{ C|373 - C|379 C|451 - C|460 }C451 - 460
18X-RAY DIFFRACTION9{ C|380 - C|450 }C380 - 450
19X-RAY DIFFRACTION10{ C|10 - C|28 D|609 - D|639 }C10 - 28
20X-RAY DIFFRACTION10{ C|10 - C|28 D|609 - D|639 }D609 - 639
21X-RAY DIFFRACTION11{ E|1 - E|8 F|2008 - F|2019 I|1 }E1 - 8
22X-RAY DIFFRACTION11{ E|1 - E|8 F|2008 - F|2019 I|1 }F2008 - 2019
23X-RAY DIFFRACTION11{ E|1 - E|8 F|2008 - F|2019 I|1 }I1
24X-RAY DIFFRACTION12{ E|2008 - E|2020 F|1 - F|8 }E2008 - 2020
25X-RAY DIFFRACTION12{ E|2008 - E|2020 F|1 - F|8 }F1 - 8

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  • 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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