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

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Basic information

Entry
Database: PDB / ID: 5cph
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
Chem-EVO / DNA gyrase subunit B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 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 21, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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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)48,6187
Polymers47,8632
Non-polymers7555
Water9,404522
1
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2503
Polymers23,9321
Non-polymers3182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3684
Polymers23,9321
Non-polymers4363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.852, 55.681, 51.569
Angle α, β, γ (deg.)90.000, 100.690, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-405-

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-EVO / (3E)-3-(pyridin-3-ylmethylidene)-1,3-dihydro-2H-indol-2-one


Mass: 222.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H10N2O
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 2.11 Å3/Da / Density % sol: 41.58 %
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: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 23, 2009
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.2→37.89 Å / Num. obs: 118625 / % possible obs: 95.6 % / Redundancy: 3.84 % / Rmerge(I) obs: 0.045 / Χ2: 0.99 / Net I/σ(I): 11.9 / Num. measured all: 458592 / Scaling rejects: 3440
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.2-1.242.720.3922.12377387131.178370.6
1.24-1.293.180.342.735016109521.1516388.6
1.29-1.353.940.2743.748792123121.1423899.9
1.35-1.423.980.2154.849471123461.0931199.9
1.42-1.514.010.162650049123801.0244399.8
1.51-1.634.040.1187.750388123610.9350499.7
1.63-1.794.060.091050505123240.8745399.7
1.79-2.054.080.06114.450998124250.8533999.7
2.05-2.594.030.04819.250486124250.9139399.8
2.59-37.893.920.02440.849114123870.9551397.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.64 Å37.89 Å
Translation1.64 Å37.89 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
d*TREKdata reduction
d*TREK9.7 W8RSSIdata scaling
MOLREP10.2.23phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KZN

1kzn


Resolution: 1.2→37.89 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.1975 / WRfactor Rwork: 0.1749 / FOM work R set: 0.8592 / SU B: 0.675 / SU ML: 0.03 / SU R Cruickshank DPI: 0.0414 / SU Rfree: 0.0436 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.194 5976 5 %RANDOM
Rwork0.1718 ---
obs0.173 112645 95.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.03 Å2 / Biso mean: 17.139 Å2 / Biso min: 5.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.16 Å2
2--0.02 Å2-0 Å2
3----0.1 Å2
Refinement stepCycle: final / Resolution: 1.2→37.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 52 522 3620
Biso mean--25.42 28.96 -
Num. residues----378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0193246
X-RAY DIFFRACTIONr_bond_other_d0.0030.023076
X-RAY DIFFRACTIONr_angle_refined_deg2.5471.9664419
X-RAY DIFFRACTIONr_angle_other_deg1.14337067
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8655404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.74624.773176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85115577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4311526
X-RAY DIFFRACTIONr_chiral_restr0.1460.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023714
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02760
X-RAY DIFFRACTIONr_mcbond_it1.7751.3571539
X-RAY DIFFRACTIONr_mcbond_other1.7711.3551538
X-RAY DIFFRACTIONr_mcangle_it2.5592.031922
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 337 -
Rwork0.341 5889 -
all-6226 -
obs--68.28 %

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