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- PDB-5d6q: Crystal structure of the ATP binding domain of S. aureus GyrB com... -

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Basic information

Entry
Database: PDB / ID: 5d6q
TitleCrystal structure of the ATP binding domain of S. aureus GyrB complexed with a ligand
ComponentsDNA gyrase subunit B
KeywordsISOMERASE/ISOMERASE INHIBITOR / DNA gyrase / GyrB / ligand / 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-57V / DNA gyrase subunit B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsZhang, J. / Yang, Q. / Cross, J.B. / Romero, J.A.C. / Ryan, M.D. / Lippa, B. / Dolle, R.E. / Andersen, O.A. / Barker, J. / Cheng, R.K. ...Zhang, J. / Yang, Q. / Cross, J.B. / Romero, J.A.C. / Ryan, M.D. / Lippa, B. / Dolle, R.E. / Andersen, O.A. / Barker, J. / Cheng, R.K. / Kahmann, J. / Felicetti, B. / Wood, M. / Scheich, C.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Discovery of Azaindole Ureas as a Novel Class of Bacterial Gyrase B Inhibitors.
Authors: Zhang, J. / Yang, Q. / Cross, J.B. / Romero, J.A. / Poutsiaka, K.M. / Epie, F. / Bevan, D. / Wang, B. / Zhang, Y. / Chavan, A. / Zhang, X. / Moy, T. / Daniel, A. / Nguyen, K. / Chamberlain, ...Authors: Zhang, J. / Yang, Q. / Cross, J.B. / Romero, J.A. / Poutsiaka, K.M. / Epie, F. / Bevan, D. / Wang, B. / Zhang, Y. / Chavan, A. / Zhang, X. / Moy, T. / Daniel, A. / Nguyen, K. / Chamberlain, B. / Carter, N. / Shotwell, J. / Silverman, J. / Metcalf, C.A. / Ryan, D. / Lippa, B. / Dolle, R.E.
History
DepositionAug 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 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_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 / _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.ptnr2_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.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _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_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)48,7249
Polymers47,8632
Non-polymers8617
Water6,503361
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)24,5566
Polymers23,9321
Non-polymers6245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.910, 55.860, 51.460
Angle α, β, γ (deg.)90.000, 100.620, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-409-

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-57V / 1-ethyl-3-{4-[(E)-2-(pyridin-3-yl)ethenyl]-5-(1H-pyrrol-2-yl)-1,3-thiazol-2-yl}urea


Mass: 339.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H17N5OS
#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.: 361 / 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: 41.68 %
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: Apr 15, 2010
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→26.64 Å / Num. obs: 60328 / % possible obs: 94.7 % / Redundancy: 1.9 % / Rpim(I) all: 0.043 / Rrim(I) all: 0.063 / Rsym value: 0.045 / Net I/av σ(I): 8.77 / Net I/σ(I): 10.4 / Num. measured all: 114950
Reflection shell

Diffraction-ID: 1 / Redundancy: 1.9 % / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.5-1.580.3452.21682787530.3310.3452.594.6
1.58-1.680.2343.21598683490.2250.2344.195.3
1.68-1.790.1574.81496978450.150.1575.895.4
1.79-1.940.0947.71401673550.090.0948.695.5
1.94-2.120.0611.21283367510.0580.0612.895.3
2.12-2.370.04812.71153960730.0470.0481395.1
2.37-2.740.03914.7995853020.0380.03914.893.3
2.74-3.350.03117.5797542920.030.03118.389.6
3.35-4.740.0316.7720337150.0290.0326.599.1
4.74-26.6370.0317.8364418930.0290.0321.691.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.73 Å26.64 Å
Translation1.73 Å26.64 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: 1.5→26.64 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.2003 / WRfactor Rwork: 0.175 / FOM work R set: 0.8522 / SU B: 1.537 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0755 / SU Rfree: 0.0772 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1979 3103 5.1 %RANDOM
Rwork0.1673 ---
obs0.1689 57219 94.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.29 Å2 / Biso mean: 19.947 Å2 / Biso min: 6.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å2-0 Å2-0.1 Å2
2---0.96 Å2-0 Å2
3---0.66 Å2
Refinement stepCycle: final / Resolution: 1.5→26.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 58 364 3468
Biso mean--30.73 30.59 -
Num. residues----378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0193301
X-RAY DIFFRACTIONr_bond_other_d0.0020.023183
X-RAY DIFFRACTIONr_angle_refined_deg2.231.9644494
X-RAY DIFFRACTIONr_angle_other_deg1.0737303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7025412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.81624.505182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0715596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2241530
X-RAY DIFFRACTIONr_chiral_restr0.1360.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023789
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02785
X-RAY DIFFRACTIONr_mcbond_it1.9151.6421553
X-RAY DIFFRACTIONr_mcbond_other1.9091.641552
X-RAY DIFFRACTIONr_mcangle_it2.7512.4491940
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 233 -
Rwork0.28 4190 -
all-4423 -
obs--94.25 %

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