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- PDB-5ctx: Crystal structure of the ATP binding domain of S. aureus GyrB com... -

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Basic information

Entry
Database: PDB / ID: 5ctx
TitleCrystal structure of the ATP binding domain of S. aureus GyrB complexed with a fragment
ComponentsDNA gyrase subunit B
KeywordsISOMERASE/ISOMERASE INHIBITOR / DNA gyrase / GyrB / fragment-based screening / structure-based design / 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-55G / DNA gyrase subunit B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsAndersen, O.A. / Barker, J. / Cheng, R.K. / Kahmann, J. / Felicetti, B. / Wood, M. / Scheich, C. / Mesleh, M. / Cross, J.B. / Zhang, J. ...Andersen, O.A. / Barker, J. / Cheng, R.K. / Kahmann, J. / Felicetti, B. / Wood, M. / Scheich, C. / Mesleh, M. / Cross, J.B. / Zhang, J. / Yang, Q. / Lippa, B. / Ryan, M.D.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2016
Title: Fragment-based discovery of DNA gyrase inhibitors targeting the ATPase subunit of GyrB.
Authors: Mesleh, M.F. / Cross, J.B. / Zhang, J. / Kahmann, J. / Andersen, O.A. / Barker, J. / Cheng, R.K. / Felicetti, B. / Wood, M. / Hadfield, A.T. / Scheich, C. / Moy, T.I. / Yang, Q. / Shotwell, ...Authors: Mesleh, M.F. / Cross, J.B. / Zhang, J. / Kahmann, J. / Andersen, O.A. / Barker, J. / Cheng, R.K. / Felicetti, B. / Wood, M. / Hadfield, A.T. / Scheich, C. / Moy, T.I. / Yang, Q. / Shotwell, J. / Nguyen, K. / Lippa, B. / Dolle, R. / Ryan, M.D.
History
DepositionJul 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Structure summary
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_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.ptnr1_symmetry / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)48,7569
Polymers47,8632
Non-polymers8937
Water6,323351
1
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1683
Polymers23,9321
Non-polymers2362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5886
Polymers23,9321
Non-polymers6565
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.892, 55.655, 51.213
Angle α, β, γ (deg.)90.000, 100.550, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-408-

HOH

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Components

#1: Protein DNA gyrase subunit B


Mass: 23931.602 Da / Num. of mol.: 2
Fragment: ATP binding domain, UNP residues 2-234 (delta 105-127)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: P0A0K8, EC: 5.99.1.3
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-55G / 4-phenyl-3-[2-(pyridin-3-yl)-1,3-thiazol-5-yl]-2,7-dihydro-6H-pyrazolo[3,4-b]pyridin-6-one


Mass: 371.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H13N5OS
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.09 Å3/Da / Density % sol: 41.19 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 40-43% MPD_P1K_P3350, 100 mM Mops/Na-Hepes, 100 mM Divalents

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 31, 2010
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→45.01 Å / Num. obs: 51605 / % possible obs: 98.8 % / Redundancy: 2.27 % / Rmerge(I) obs: 0.046 / Χ2: 0.99 / Net I/σ(I): 10.4 / Num. measured all: 117786 / Scaling rejects: 885
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.6-1.662.190.2972.31109250570.74098.4
1.66-1.722.210.2532.71140651600.81099
1.72-1.82.210.2113.31143751770.89199.3
1.8-1.92.220.183.81150151760.93299.5
1.9-2.022.240.1384.91163051950.93999.8
2.02-2.172.270.1036.41181251890.951799.8
2.17-2.392.280.0748.81198652380.9140100
2.39-2.742.310.05512.51212752100.9510699.7
2.74-3.452.340.03719.81234251771.1121398.4
3.45-45.012.380.02637.61245350261.6149793.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.92 Å45.01 Å
Translation1.92 Å45.01 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
d*TREKdata reduction
d*TREK9.7 W8RSSIdata scaling
MOLREP10.2.35phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KZN

1kzn


Resolution: 1.6→45.01 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.1886 / FOM work R set: 0.8335 / SU B: 2.041 / SU ML: 0.07 / SU R Cruickshank DPI: 0.0973 / SU Rfree: 0.0971 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2195 2623 5.1 %RANDOM
Rwork0.1849 ---
obs0.1867 48976 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.84 Å2 / Biso mean: 26.594 Å2 / Biso min: 13.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å2-0.08 Å2
2---0.55 Å2-0 Å2
3---0.45 Å2
Refinement stepCycle: final / Resolution: 1.6→45.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3072 0 61 351 3484
Biso mean--39.89 36.1 -
Num. residues----381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193304
X-RAY DIFFRACTIONr_bond_other_d0.0020.023168
X-RAY DIFFRACTIONr_angle_refined_deg2.0471.9684496
X-RAY DIFFRACTIONr_angle_other_deg1.04437279
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5885413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.41424.693179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11115597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7141527
X-RAY DIFFRACTIONr_chiral_restr0.1160.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023769
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02766
X-RAY DIFFRACTIONr_mcbond_it2.2632.31558
X-RAY DIFFRACTIONr_mcbond_other2.2622.2981557
X-RAY DIFFRACTIONr_mcangle_it3.3683.4341947
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 207 -
Rwork0.382 3544 -
all-3751 -
obs--98.43 %

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