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

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Basic information

Entry
Database: PDB / ID: 5ctw
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 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
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 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
2-(butanoylamino)thiophene-3-carboxamide / DNA gyrase subunit B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.48 Å
AuthorsAndersen, O.A. / Barker, J. / Hadfield, A.T. / Cheng, R.K. / Kahmann, J. / Felicetti, B. / Wood, M. / Scheich, C. / Mesleh, M. / Cross, J.B. ...Andersen, O.A. / Barker, J. / Hadfield, A.T. / 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: Database references
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 / citation / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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.ptnr1_symmetry / _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.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.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

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)48,99813
Polymers47,8632
Non-polymers1,13511
Water4,071226
1
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4406
Polymers23,9321
Non-polymers5085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5587
Polymers23,9321
Non-polymers6276
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.320, 56.079, 50.183
Angle α, β, γ (deg.)90.000, 98.990, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-483-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA gyrase subunit B


Mass: 23931.602 Da / Num. of mol.: 2
Fragment: ATP binding domain, UNP residues 2-234 (delta105-127)
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

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Non-polymers , 5 types, 237 molecules

#2: Chemical ChemComp-55D / 2-(butanoylamino)thiophene-3-carboxamide


Mass: 212.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12N2O2S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.05 Å3/Da / Density % sol: 40.05 %
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: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 13, 2012
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.475→27.499 Å / Num. all: 58540 / Num. obs: 58540 / % possible obs: 89.9 % / Redundancy: 2.9 % / Rpim(I) all: 0.028 / Rrim(I) all: 0.05 / Rsym value: 0.037 / Net I/av σ(I): 8.857 / Net I/σ(I): 11 / Num. measured all: 172355
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.48-1.512.10.3941.9552526780.2960.394256.2
1.51-1.562.20.2782.5693632170.2280.2782.469.8
1.56-1.62.40.2253.2888137260.1810.225381.7
1.6-1.652.90.193.91188440690.1550.193.692.7
1.65-1.73.10.1764.11277541410.1360.1764.296.2
1.7-1.763.10.145.21250039930.1080.145.296.1
1.76-1.833.20.11861224338600.0890.1186.496.6
1.83-1.93.10.0997.11152836940.0720.0997.996.5
1.9-1.992.80.0857.8956634360.0620.0859.292.9
1.99-2.0930.079.6997533270.0510.0711.394
2.09-2.23.30.05511.91093932930.040.05513.898.1
2.2-2.333.30.04713.31008930970.0350.04715.797.6
2.33-2.493.20.04215935829550.0310.04216.797.7
2.49-2.693.10.03817.2830527030.0280.03817.997.2
2.69-2.952.70.03716.5608722910.0270.03718.689.4
2.95-3.33.30.0320.8754623100.0210.0323.398.8
3.3-3.813.30.02721.6671920360.0190.02726.998.5
3.81-4.673.10.02820.3521117070.020.02827.396.8
4.67-6.62.90.03119.1358012300.0220.03125.791.6
6.6-27.4993.50.03613.627087770.0240.03628.698.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
SCALA3.3.20data scaling
MOLREPphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KZN

1kzn


Resolution: 1.48→27.5 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2853 / WRfactor Rwork: 0.2328 / FOM work R set: 0.7282 / SU B: 2.689 / SU ML: 0.095 / SU R Cruickshank DPI: 0.0976 / SU Rfree: 0.1031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2961 5.1 %RANDOM
Rwork0.2162 ---
obs0.2187 55576 89.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.73 Å2 / Biso mean: 27.734 Å2 / Biso min: 11.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å2-0 Å2-1.82 Å2
2--1.04 Å2-0 Å2
3---0.25 Å2
Refinement stepCycle: final / Resolution: 1.48→27.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3093 0 72 227 3392
Biso mean--38.52 34.06 -
Num. residues----384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193332
X-RAY DIFFRACTIONr_bond_other_d0.0020.023212
X-RAY DIFFRACTIONr_angle_refined_deg1.9641.974534
X-RAY DIFFRACTIONr_angle_other_deg1.08637381
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25417
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.57224.916179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34215601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7481525
X-RAY DIFFRACTIONr_chiral_restr0.1170.2511
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023797
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02758
X-RAY DIFFRACTIONr_mcbond_it2.6242.4841572
X-RAY DIFFRACTIONr_mcbond_other2.6222.4811571
X-RAY DIFFRACTIONr_mcangle_it3.6413.7121965
LS refinement shellResolution: 1.475→1.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 125 -
Rwork0.401 2540 -
all-2665 -
obs--55.57 %

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