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- PDB-5d7d: Crystal structure of the ATP binding domain of S. aureus GyrB com... -

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Basic information

Entry
Database: PDB / ID: 5d7d
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-57X / DNA gyrase subunit B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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: Acs Med.Chem.Lett. / Year: 2015
Title: Discovery of Indazole Derivatives as a Novel Class of Bacterial Gyrase B Inhibitors.
Authors: Zhang, J. / Yang, Q. / Romero, J.A. / Cross, J. / Wang, B. / Poutsiaka, K.M. / Epie, F. / Bevan, D. / Wu, Y. / Moy, T. / Daniel, A. / Chamberlain, B. / Carter, N. / Shotwell, J. / Arya, A. / ...Authors: Zhang, J. / Yang, Q. / Romero, J.A. / Cross, J. / Wang, B. / Poutsiaka, K.M. / Epie, F. / Bevan, D. / Wu, Y. / Moy, T. / Daniel, A. / Chamberlain, B. / Carter, N. / Shotwell, J. / Arya, A. / Kumar, V. / Silverman, J. / Nguyen, K. / Metcalf, C.A. / Ryan, D. / Lippa, B. / Dolle, R.E.
History
DepositionAug 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
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 / 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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_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_label_seq_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)49,25217
Polymers47,8632
Non-polymers1,38915
Water5,224290
1
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6389
Polymers23,9321
Non-polymers7068
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6148
Polymers23,9321
Non-polymers6827
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.300, 55.446, 51.029
Angle α, β, γ (deg.)90.000, 100.950, 90.000
Int Tables number5
Space group name H-MC121

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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, 305 molecules

#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-57X / 7-propyl-3-[2-(pyridin-3-yl)-1,3-thiazol-5-yl]-1,7-dihydro-6H-pyrazolo[3,4-b]pyridin-6-one


Mass: 337.399 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H15N5OS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 40.84 %
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: Feb 3, 2011
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→50.1 Å / Num. obs: 51220 / % possible obs: 98.5 % / Redundancy: 2.68 % / Rmerge(I) obs: 0.036 / Χ2: 0.98 / Net I/σ(I): 12 / Num. measured all: 138531 / Scaling rejects: 1039
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.6-1.662.440.4922.21136046461.241290.3
1.66-1.722.610.3992.51346051551.141499.9
1.72-1.82.630.2833.41361951661.05899.9
1.8-1.92.650.2034.61376251771.0438100
1.9-2.022.660.1426.31383651511.0214799.7
2.02-2.172.680.0999.2140995182119799.7
2.17-2.392.720.08411.81423251800.9114299.8
2.39-2.742.770.05715.91451752090.827099.8
2.74-3.452.820.038231471751900.818699.3
3.45-50.12.830.02736.81492951640.9132596.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.98 Å37.58 Å
Translation1.98 Å37.58 Å

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Processing

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

1kzn


Resolution: 1.6→50.1 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / WRfactor Rfree: 0.1948 / WRfactor Rwork: 0.1655 / FOM work R set: 0.8382 / SU B: 4.486 / SU ML: 0.068 / SU R Cruickshank DPI: 0.088 / SU Rfree: 0.0868 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1946 2607 5.1 %RANDOM
Rwork0.1654 ---
obs0.1669 48608 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.61 Å2 / Biso mean: 29.55 Å2 / Biso min: 15.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0 Å2-0.43 Å2
2---0.04 Å20 Å2
3---0.26 Å2
Refinement stepCycle: final / Resolution: 1.6→50.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3076 0 89 292 3457
Biso mean--35.29 39.24 -
Num. residues----382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0193396
X-RAY DIFFRACTIONr_bond_other_d0.0020.023246
X-RAY DIFFRACTIONr_angle_refined_deg2.5271.9754639
X-RAY DIFFRACTIONr_angle_other_deg1.18937475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3585433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.94925186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58215614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1861526
X-RAY DIFFRACTIONr_chiral_restr0.1470.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023906
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02786
X-RAY DIFFRACTIONr_mcbond_it2.2372.311584
X-RAY DIFFRACTIONr_mcbond_other2.222.3081583
X-RAY DIFFRACTIONr_mcangle_it3.3223.4481984
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.465 178 -
Rwork0.387 3153 -
all-3331 -
obs--86.95 %
Refinement TLS params.Method: refined / Origin x: -9.1451 Å / Origin y: -28.2493 Å / Origin z: 8.6411 Å
111213212223313233
T0.0195 Å20.0166 Å2-0.0151 Å2-0.0388 Å2-0.0111 Å2--0.0162 Å2
L0.1863 °20.1332 °20.1314 °2-0.0963 °20.0908 °2--0.177 °2
S-0.0024 Å °-0.0121 Å °0.0281 Å °-0.0027 Å °-0.0164 Å °0.0211 Å °-0.0002 Å °0.0052 Å °0.0188 Å °

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