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

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Basic information

Entry
Database: PDB / ID: 5ctu
TitleCrystal structure of the ATP binding domain of S. aureus GyrB complexed with a fragment
ComponentsDNA gyrase subunit B
KeywordsISOMERASE / DNA gyrase / GyrB / fragment-based screening / structure-based design
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
5-(thiophen-2-yl)thieno[2,3-d]pyrimidin-4(1H)-one / DNA gyrase subunit B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 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: 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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)48,7469
Polymers47,8632
Non-polymers8837
Water8,629479
1
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3204
Polymers23,9321
Non-polymers3883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4275
Polymers23,9321
Non-polymers4954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.660, 55.650, 51.140
Angle α, β, γ (deg.)90.000, 101.010, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-404-

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 (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

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Non-polymers , 5 types, 486 molecules

#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-54X / 5-(thiophen-2-yl)thieno[2,3-d]pyrimidin-4(1H)-one


Mass: 234.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H6N2OS2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.08 Å3/Da / Density % sol: 40.91 %
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 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 27, 2010
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.45→25.858 Å / Num. all: 69300 / Num. obs: 69300 / % possible obs: 99.3 % / Redundancy: 3.3 % / Rpim(I) all: 0.091 / Rrim(I) all: 0.169 / Rsym value: 0.141 / Net I/av σ(I): 2.724 / Net I/σ(I): 5.5 / Num. measured all: 231398
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
1.45-1.533.30.481.433531100770.3050.482.299
1.53-1.623.30.3451.93174695140.2210.3453.299.3
1.62-1.733.40.2542.43031689660.1620.2544.199.5
1.73-1.873.40.1962.92864184120.1250.1965.299.8
1.87-2.053.40.1533.32640777200.0970.1536.599.8
2.05-2.293.30.1423.32329469800.0910.1427.399.8
2.29-2.653.10.1243.51922862040.0830.1247.599.7
2.65-3.243.30.10641707151900.0670.1068.398.8
3.24-4.593.50.0974.41406740770.0620.0978.999.8
4.59-26.4433.30.0914.9709721600.060.0918.794

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.55 Å25.1 Å
Translation1.55 Å25.1 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
SCALA3.3.9data scaling
MOLREP10.2.23phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KZN

1kzn


Resolution: 1.45→25.86 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2271 / WRfactor Rwork: 0.1967 / FOM work R set: 0.8541 / SU B: 1.419 / SU ML: 0.054 / SU R Cruickshank DPI: 0.0699 / SU Rfree: 0.0712 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 3472 5 %RANDOM
Rwork0.1762 ---
obs0.1776 65826 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.12 Å2 / Biso mean: 12.134 Å2 / Biso min: 2.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20.31 Å2
2---0.74 Å2-0 Å2
3---0.41 Å2
Refinement stepCycle: final / Resolution: 1.45→25.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3083 0 56 479 3618
Biso mean--23.85 24.36 -
Num. residues----384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193256
X-RAY DIFFRACTIONr_bond_other_d0.0020.023120
X-RAY DIFFRACTIONr_angle_refined_deg2.2851.9674418
X-RAY DIFFRACTIONr_angle_other_deg1.12237149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5775398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56124.419172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01315578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.41528
X-RAY DIFFRACTIONr_chiral_restr0.1360.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023688
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02754
X-RAY DIFFRACTIONr_mcbond_it1.3560.9111552
X-RAY DIFFRACTIONr_mcbond_other1.3470.9091551
X-RAY DIFFRACTIONr_mcangle_it2.081.3541932
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 245 -
Rwork0.276 4808 -
all-5053 -
obs--98.94 %

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