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- PDB-3u2k: S. aureus GyrB ATPase domain in complex with a small molecule inh... -

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Basic information

Entry
Database: PDB / ID: 3u2k
TitleS. aureus GyrB ATPase domain in complex with a 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-087 / DNA gyrase subunit B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 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)46,09810
Polymers45,0902
Non-polymers1,0078
Water7,927440
1
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0495
Polymers22,5451
Non-polymers5044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0495
Polymers22,5451
Non-polymers5044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.175, 55.497, 51.349
Angle α, β, γ (deg.)90.000, 100.670, 90.000
Int Tables number5
Space group name H-MC121

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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-087 / 2-chloro-6-(4-{[(3,4-dichloro-5-methyl-1H-pyrrol-2-yl)carbonyl]amino}piperidin-1-yl)pyridine-4-carboxamide


Mass: 430.716 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18Cl3N5O2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.22 Å3/Da / Density % sol: 44.67 %
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: Nov 12, 2010 / 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: 1.64→35.175 Å / Num. all: 124850 / Num. obs: 43084 / % possible obs: 88.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rsym value: 0.024 / Net I/σ(I): 21.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.64-1.731.90.184.4983951360.1872.6
1.73-1.831.90.1345.91029653310.13479.4
1.83-1.961.90.0849.41062154760.08487
1.96-2.112.20.05414.61197753970.05492.1
2.11-2.312.70.0419.51346050590.0493.3
2.31-2.593.10.03422.31424046310.03494.7
2.59-2.993.80.02925.71578241360.02995.6
2.99-3.663.80.019361357435750.01996.7
3.66-5.183.70.01638.71029527720.01697.3
5.18-35.1753.60.01836.4561515710.01897.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
SCALA3.3.15data scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→35.17 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.1683 / WRfactor Rwork: 0.1466 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.9054 / SU B: 3.216 / SU ML: 0.053 / SU R Cruickshank DPI: 0.1018 / SU Rfree: 0.0949 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.182 2181 5.1 %RANDOM
Rwork0.1562 ---
obs0.1575 42877 88.15 %-
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: 49.56 Å2 / Biso mean: 16.4114 Å2 / Biso min: 4.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å2-0.19 Å2
2--0.11 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.64→35.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3058 0 60 440 3558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223273
X-RAY DIFFRACTIONr_bond_other_d0.0010.022143
X-RAY DIFFRACTIONr_angle_refined_deg1.0621.9664456
X-RAY DIFFRACTIONr_angle_other_deg0.76935232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2655400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.62924.885174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1215571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9281524
X-RAY DIFFRACTIONr_chiral_restr0.0660.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023726
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02646
X-RAY DIFFRACTIONr_mcbond_it0.4851.51944
X-RAY DIFFRACTIONr_mcbond_other0.1081.5800
X-RAY DIFFRACTIONr_mcangle_it0.96823173
X-RAY DIFFRACTIONr_scbond_it1.86931329
X-RAY DIFFRACTIONr_scangle_it3.2374.51283
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 129 -
Rwork0.19 2397 -
all-2526 -
obs--70.94 %
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)
10.4528-0.01790.06790.5285-0.01440.5835-0.00010.03720.00320.0048-0.02450.05330.02210.04120.02460.0041-0.00040.00930.0088-0.00130.037.12412.05920.035
20.85670.31470.16280.80490.15120.6984-0.08590.05830.0896-0.08580.02810.1024-0.04690.06540.05780.0186-0.0087-0.01410.01150.01650.035725.945-12.3192.699
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 230
2X-RAY DIFFRACTION2B20 - 230

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