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- PDB-5d7c: Crystal structure of the ATP binding domain of S. aureus GyrB com... -

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Basic information

Entry
Database: PDB / ID: 5d7c
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 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-57W / DNA gyrase subunit B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 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 13, 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 / 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 / _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_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 / _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.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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)49,24716
Polymers47,8632
Non-polymers1,38414
Water6,161342
1
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5515
Polymers23,9321
Non-polymers6194
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,69611
Polymers23,9321
Non-polymers76510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.803, 55.485, 51.422
Angle α, β, γ (deg.)90.000, 100.770, 90.000
Int Tables number5
Space group name H-MC121

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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-57W / 1-ethyl-3-[1-(pyridin-2-yl)-6-(pyridin-3-yl)-1H-pyrrolo[3,2-b]pyridin-3-yl]urea


Mass: 358.397 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H18N6O
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.09 Å3/Da / Density % sol: 41.17 %
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: Sep 2, 2010
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→45.19 Å / Num. obs: 55678 / % possible obs: 96.8 % / Redundancy: 2.35 % / Rmerge(I) obs: 0.044 / Χ2: 0.98 / Net I/σ(I): 11.8 / Num. measured all: 132107 / Scaling rejects: 991
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.55-1.611.90.2483.7868045571.03279.3
1.61-1.672.290.2184.41298556791799.7
1.67-1.752.310.1851320057130.94899.9
1.75-1.842.330.1476.11337457270.911499.8
1.84-1.952.350.1247.41346557110.8823100
1.95-2.12.390.0959.41372457330.851399.9
2.1-2.322.420.07112.61384857140.863199.7
2.32-2.652.450.06614.41402456960.915499
2.65-3.342.50.05318.81427056620.9912598
3.34-45.192.520.04132.11453754861.4171493.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.85 Å37.78 Å
Translation1.85 Å37.78 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
d*TREKdata reduction
d*TREK9.9.8.6 W9RSSIdata scaling
MOLREP10.2.35phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KZN

1kzn


Resolution: 1.55→37.78 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2101 / WRfactor Rwork: 0.1834 / FOM work R set: 0.863 / SU B: 3.257 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0833 / SU Rfree: 0.0828 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1993 2846 5.1 %RANDOM
Rwork0.1712 ---
obs0.1726 52823 96.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.05 Å2 / Biso mean: 23.818 Å2 / Biso min: 10.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20.39 Å2
2--0.02 Å20 Å2
3----0.34 Å2
Refinement stepCycle: final / Resolution: 1.55→37.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 94 345 3485
Biso mean--29.52 34.93 -
Num. residues----378
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0193301
X-RAY DIFFRACTIONr_bond_other_d0.0020.023172
X-RAY DIFFRACTIONr_angle_refined_deg2.7341.9774488
X-RAY DIFFRACTIONr_angle_other_deg1.39437270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6065404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.34324.463177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87615588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2341529
X-RAY DIFFRACTIONr_chiral_restr0.1730.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.023764
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02785
X-RAY DIFFRACTIONr_mcbond_it1.8221.6941543
X-RAY DIFFRACTIONr_mcbond_other1.8151.6921542
X-RAY DIFFRACTIONr_mcangle_it2.6942.5281925
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 169 -
Rwork0.342 2977 -
all-3146 -
obs--73.94 %
Refinement TLS params.Method: refined / Origin x: -4.3524 Å / Origin y: -0.5347 Å / Origin z: -16.5461 Å
111213212223313233
T0.0299 Å20.0181 Å2-0.0324 Å2-0.02 Å2-0.0104 Å2--0.0539 Å2
L0.1529 °20.0985 °20.0864 °2-0.0639 °20.0523 °2--0.1423 °2
S-0.0083 Å °-0.0069 Å °0.0278 Å °-0.0064 Å °-0.0086 Å °0.018 Å °0.0005 Å °0.0066 Å °0.0169 Å °

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