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- PDB-2y3p: Crystal structure of N-terminal domain of GyrA with the antibioti... -

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Basic information

Entry
Database: PDB / ID: 2y3p
TitleCrystal structure of N-terminal domain of GyrA with the antibiotic simocyclinone D8
ComponentsDNA GYRASE SUBUNIT A
KeywordsISOMERASE / AMINOCOUMARIN ANTIBIOTIC
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / cytoplasm
Similarity search - Function
Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / Gyrase A; domain 2 - #40 / 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. ...Topoisomerase II; domain 5 / Topoisomerase II, domain 5 / Topoisomerase, domain 3 / Topoisomerase; domain 3 / Gyrase A; domain 2 - #40 / 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 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-like domain superfamily / Gyrase A; domain 2 / Alpha-Beta Complex / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
SIMOCYCLINONE D8 / DNA gyrase subunit A
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsEdwards, M.J. / Flatman, R.H. / Mitchenall, L.A. / Stevenson, C.E.M. / Le, T.B.K. / Clarke, T.A. / McKay, A.R. / Fiedler, H.-P. / Buttner, M.J. / Lawson, D.M. / Maxwell, A.
Citation
Journal: Science / Year: 2009
Title: A Crystal Structure of the Bifunctional Antibiotic Simocyclinone D8, Bound to DNA Gyrase.
Authors: Edwards, M.J. / Flatman, R.H. / Mitchenall, L.A. / Stevenson, C.E.M. / Le, T.B.K. / Clarke, T.A. / Mckay, A.R. / Fiedler, H.-P. / Buttner, M.J. / Lawson, D.M. / Maxwell, A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and Preliminary X-Ray Analysis of a Complex Formed between the Antibiotic Simocyclinone D8 and the DNA Breakage-Reunion Domain of Escherichia Coli DNA Gyrase.
Authors: Edwards, M.J. / Flatman, R.H. / Mitchenall, L.A. / Stevenson, C.E.M. / Maxwell, A. / Lawson, D.M.
History
DepositionDec 22, 2010Deposition site: PDBE / Processing site: PDBE
SupersessionDec 29, 2010ID: 2WL2
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_symmetry / _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_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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_symmetry / _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 GYRASE SUBUNIT A
B: DNA GYRASE SUBUNIT A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,2088
Polymers117,2462
Non-polymers1,9626
Water1,72996
1
A: DNA GYRASE SUBUNIT A
B: DNA GYRASE SUBUNIT A
hetero molecules

A: DNA GYRASE SUBUNIT A
B: DNA GYRASE SUBUNIT A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,41616
Polymers234,4924
Non-polymers3,92412
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area16370 Å2
ΔGint-114.4 kcal/mol
Surface area85510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.910, 153.090, 177.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.158, 0.983, -0.098), (0.981, -0.168, -0.096), (-0.111, -0.081, -0.99)
Vector: -35.25542, 46.29, 46.39528)

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Components

#1: Protein DNA GYRASE SUBUNIT A / GYRA


Mass: 58623.027 Da / Num. of mol.: 2 / Fragment: N-TERMINAL 59KDA DOMAIN, RESIDUES 2-523
Source method: isolated from a genetically manipulated source
Details: COMPRISES RESIDUES 2-523 OF WILD TYPE SEQUENCE / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: JMTACA / Plasmid: PRJR10.18 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B843 / Variant (production host): PLYSS / References: UniProt: P0AES5, EC: 5.99.1.3
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SM8 / SIMOCYCLINONE D8


Mass: 932.275 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C46H42ClNO18
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 4.18 Å3/Da / Density % sol: 70.6 % / Description: NONE
Crystal growpH: 8.5
Details: 6% (W/V) PEG 8000, 30% (V/V) GLYCEROL IN 100 MM TRIS-HCL PH 8.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.542
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 12, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.62→27.47 Å / Num. obs: 58959 / % possible obs: 99.8 % / Observed criterion σ(I): -9 / Redundancy: 5.1 % / Biso Wilson estimate: 46.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14
Reflection shellResolution: 2.62→2.76 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AB4

1ab4


Resolution: 2.62→27.47 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / SU B: 21.13 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE SIMOCYCLINONE D8 EFFECTIVELY CROSSLINKS A PAIR OF GYRA59 DIMERS ACROSS A CRYSTALLOGRAPHIC 2-FOLD AXIS. THE RESULTANT COMPLEX CONTAINS 4 ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE SIMOCYCLINONE D8 EFFECTIVELY CROSSLINKS A PAIR OF GYRA59 DIMERS ACROSS A CRYSTALLOGRAPHIC 2-FOLD AXIS. THE RESULTANT COMPLEX CONTAINS 4 MOLECULES OF SIMOCYCLINONE D8, WITH EACH LIGAND MAKING CONTACT WITH SUBUNITS FROM OPPOSING DIMERS SUCH THAT EACH GYRA59 SUBUNIT BINDS THE POLYKETIDE AND THE AMINOCOUMARIN MOIETIES, RESPECTIVELY, OF TWO SEPARATE SIMOCYCLINON D8 MOLECULES. THE TETRAMER IS ALSO OBSERVED IN SOLUTION AT HIGH LIGAND TO PROTEIN RATIOS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24118 2967 5 %RANDOM
Rwork0.20203 ---
obs0.20399 55953 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.62→27.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7721 0 136 96 7953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0217990
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.94710870
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4295998
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23823.706367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.405151333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6781575
X-RAY DIFFRACTIONr_chiral_restr0.1960.21245
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216073
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_it0.6961.54980
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36227983
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.46933010
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2044.52881
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 2.62→2.687 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 194 -
Rwork0.325 4075 -
obs--99.72 %
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)
11.9306-0.6624-0.0852.16440.80631.38230.01990.047-0.0241-0.08110.08480.044-0.07-0.0601-0.10470.0674-0.00320.0080.11590.05860.0365-22.8439.183132.2517
24.02850.73092.28350.59760.53722.1779-0.08530.06060.21180.17120.0768-0.0584-0.2530.08540.00850.25330.02550.06810.1494-0.02310.1453-9.54858.556649.9168
31.10620.86790.15983.49110.65360.4464-0.0560.1598-0.2157-0.32390.06830.57230.1518-0.2611-0.01230.3125-0.0291-0.0880.43460.09610.3212-49.908120.625525.1594
43.15940.84571.05030.57530.71091.04570.2406-0.29690.00140.277-0.23860.15470.3343-0.3889-0.0020.2298-0.0120.09350.40210.0920.2856-44.172534.052441.459
50.48032.30161.514711.04067.2674.78380.3008-0.21880.21441.5466-1.02571.08711.0077-0.66170.72490.93780.0475-0.0020.53910.14890.79913.14357.814435.7171
61.2014-0.13850.04421.1526-0.06571.51910.023-0.0234-0.0244-0.03610.0143-0.03790.13650.0449-0.03730.1202-0.0322-0.03470.05110.01470.0446-1.546713.685311.9407
70.51740.8769-0.90372.6589-2.62243.03790.05340.03860.14460.009-0.1395-0.2050.04940.29820.08610.1485-0.00460.01930.28190.0130.245716.107226.1853-7.8601
83.1848-0.1737-1.54530.9847-0.0741.0017-0.198-0.2029-0.57540.11140.04710.39190.2896-0.1360.15090.4245-0.0923-0.05570.29730.08420.319-25.7845-8.50525.281
90.16280.4027-0.44612.4428-1.00081.8869-0.10020.1608-0.0762-0.15090.15380.16320.3749-0.5582-0.05360.3696-0.076-0.06480.2774-0.05490.2973-12.7182-6.28746.9504
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 204
2X-RAY DIFFRACTION2A205 - 333
3X-RAY DIFFRACTION3A334 - 469
4X-RAY DIFFRACTION4A470 - 522
5X-RAY DIFFRACTION5B13 - 22
6X-RAY DIFFRACTION6B23 - 229
7X-RAY DIFFRACTION7B230 - 337
8X-RAY DIFFRACTION8B338 - 468
9X-RAY DIFFRACTION9B469 - 522

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