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- PDB-3u2d: S. aureus GyrB ATPase domain in complex with small molecule inhibitor -

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Basic information

Entry
Database: PDB / ID: 3u2d
TitleS. aureus GyrB ATPase domain in complex with small molecule inhibitor
ComponentsDNA gyrase subunit B
KeywordsISOMERASE/ISOMERASE INHIBITOR / protein-inhibitor complex / ATP-binding / structure-based drug design / antimicrobial / ISOMERASE-ISOMERASE INHIBITOR complex
Function / homology
Function and homology information


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 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 / 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. ...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 / 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-like ATPase, C-terminal domain / Heat Shock Protein 90 / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-08B / DNA gyrase subunit B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsBoriack-Sjodin, P.A. / Prince, D.B. / Eakin, A.E. / Sherer, B.A.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2012
Title: Pyrrolamide DNA gyrase inhibitors: fragment-based nuclear magnetic resonance screening to identify antibacterial agents.
Authors: Eakin, A.E. / Green, O. / Hales, N. / Walkup, G.K. / Bist, S. / Singh, A. / Mullen, G. / Bryant, J. / Embrey, K. / Gao, N. / Breeze, A. / Timms, D. / Andrews, B. / Uria-Nickelsen, M. / ...Authors: Eakin, A.E. / Green, O. / Hales, N. / Walkup, G.K. / Bist, S. / Singh, A. / Mullen, G. / Bryant, J. / Embrey, K. / Gao, N. / Breeze, A. / Timms, D. / Andrews, B. / Uria-Nickelsen, M. / Demeritt, J. / Loch, J.T. / Hull, K. / Blodgett, A. / Illingworth, R.N. / Prince, B. / Boriack-Sjodin, P.A. / Hauck, S. / Macpherson, L.J. / Ni, H. / Sherer, B.
History
DepositionOct 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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_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_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _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 gyrase subunit B
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0048
Polymers45,0902
Non-polymers9146
Water5,837324
1
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0024
Polymers22,5451
Non-polymers4573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0024
Polymers22,5451
Non-polymers4573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.487, 55.646, 51.103
Angle α, β, γ (deg.)90.000, 100.380, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-381-

HOH

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Components

#1: Protein DNA gyrase subunit B


Mass: 22545.219 Da / Num. of mol.: 2
Fragment: ATPase domain with loop deletion, UNP residues 14-104 and 128-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB / Plasmid: pT73.3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A0K8, EC: 5.99.1.3
#2: Chemical ChemComp-08B / 4-bromo-5-methyl-N-[1-(3-nitropyridin-2-yl)piperidin-4-yl]-1H-pyrrole-2-carboxamide


Mass: 408.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H18BrN5O3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 293 K / Method: sitting drop, inhibitor soak / pH: 7.5
Details: 19-30% PEG3350, 0.1MHepes, pH 7.5, 0.2M MgCl2, sitting drop, inhibitor soak, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 4, 2008 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→51.77 Å / Num. obs: 33210 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.02 % / Rmerge(I) obs: 0.095 / Χ2: 0.99 / Net I/σ(I): 6.6 / Scaling rejects: 759
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.85-1.922.570.3352.2807331201.1892.4
1.92-1.993.040.2842.8996332631.0996.7
1.99-2.083.040.2383.31004732831.0497.2
2.08-2.193.040.1874.11007432940.9997.5
2.19-2.333.040.1535.11021433390.9898
2.33-2.513.070.1395.71029633280.9798.4
2.51-2.763.080.135.91043033680.9599
2.76-3.163.090.1176.61050833700.9899.3
3.16-3.993.070.068121064234290.8599.7
3.99-51.773.080.05116.21071834160.8997.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
d*TREK9.8Ldata reduction
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
JDirectordata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→51.77 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2194 / WRfactor Rwork: 0.1901 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.8507 / SU B: 6.376 / SU ML: 0.094 / SU R Cruickshank DPI: 0.1717 / SU Rfree: 0.1476 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2322 1682 5.1 %RANDOM
Rwork0.2007 ---
obs0.2024 33063 97.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 62.25 Å2 / Biso mean: 26.337 Å2 / Biso min: 10.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20.04 Å2
2--0.1 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.85→51.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3060 0 54 324 3438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223246
X-RAY DIFFRACTIONr_bond_other_d0.0010.022132
X-RAY DIFFRACTIONr_angle_refined_deg0.9391.9644412
X-RAY DIFFRACTIONr_angle_other_deg0.75135199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.965395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3724.798173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.35615567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5981525
X-RAY DIFFRACTIONr_chiral_restr0.0610.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023680
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02641
X-RAY DIFFRACTIONr_mcbond_it0.3311.51931
X-RAY DIFFRACTIONr_mcbond_other0.0681.5796
X-RAY DIFFRACTIONr_mcangle_it0.65223147
X-RAY DIFFRACTIONr_scbond_it1.16631315
X-RAY DIFFRACTIONr_scangle_it2.0454.51265
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 101 -
Rwork0.224 2164 -
all-2265 -
obs--90.24 %
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)
10.6402-0.02180.01040.7767-0.12150.71380.00450.00750.0058-0.0004-0.02140.07630.00310.02430.01690.00530.0010.0040.03070.00140.00827.35511.6720.09
21.1180.29430.11171.21590.21220.8494-0.08590.08250.1195-0.08990.01110.1712-0.06460.00420.07480.0341-0.0051-0.01640.03810.01780.034325.542-13.0162.198
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 230
2X-RAY DIFFRACTION2B20 - 230

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