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- PDB-3ttz: Crystal structure of a topoisomerase ATPase inhibitor -

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Basic information

Entry
Database: PDB / ID: 3ttz
TitleCrystal structure of a topoisomerase ATPase inhibitor
ComponentsDNA gyrase subunit B
KeywordsISOMERASE/ISOMERASE INHIBITOR / protein-inhibitor complex / ATP-binding / structure-based drug design / antimicrobial / 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-07N / DNA gyrase subunit B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.63 Å
AuthorsBoriack-Sjodin, P.A. / Read, J. / Eakin, A.E. / Sherer, B.A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Pyrrolamide DNA gyrase inhibitors: Optimization of antibacterial activity and efficacy.
Authors: Sherer, B.A. / Hull, K. / Green, O. / Basarab, G. / Hauck, S. / Hill, P. / Loch, J.T. / Mullen, G. / Bist, S. / Bryant, J. / Boriack-Sjodin, A. / Read, J. / Degrace, N. / Uria-Nickelsen, M. ...Authors: Sherer, B.A. / Hull, K. / Green, O. / Basarab, G. / Hauck, S. / Hill, P. / Loch, J.T. / Mullen, G. / Bist, S. / Bryant, J. / Boriack-Sjodin, A. / Read, J. / Degrace, N. / Uria-Nickelsen, M. / Illingworth, R.N. / Eakin, A.E.
History
DepositionSep 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2011Group: Database references
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_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_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_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 / _struct_conn.pdbx_dist_value / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_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)46,0559
Polymers45,0902
Non-polymers9647
Water7,116395
1
A: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0154
Polymers22,5451
Non-polymers4703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA gyrase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0395
Polymers22,5451
Non-polymers4944
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.178, 55.629, 51.216
Angle α, β, γ (deg.)90.000, 100.370, 90.000
Int Tables number5
Space group name H-MC121
Detailswhen truncated, this protein is a monomer, there are 2 monomers in the asymmetric unit. Native protein is heterotetramer with GyrA.

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Components

#1: Protein DNA gyrase subunit B


Mass: 22545.219 Da / Num. of mol.: 2
Fragment: ATPase domain with loop deletion, UNP residues 14-104 and 128-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: gyrB / Plasmid: pT73.3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A0K8, EC: 5.99.1.3
#2: Chemical ChemComp-07N / 2-[(3S,4R)-4-{[(3,4-dichloro-5-methyl-1H-pyrrol-2-yl)carbonyl]amino}-3-fluoropiperidin-1-yl]-1,3-thiazole-5-carboxylic acid


Mass: 421.274 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15Cl2FN4O3S
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 293 K / Method: inhibitor soak / pH: 7.5
Details: 19-30% PEG3350, 0.1MHepes, pH 7.5, 0.2M MgCl2, inhibitor soak, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 12, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.63→51.739 Å / Num. all: 44473 / Num. obs: 44473 / % possible obs: 90.2 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rsym value: 0.027 / Net I/σ(I): 18.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.63-1.721.80.1674.7977553710.16775.2
1.72-1.821.90.1246.41035555590.12482.2
1.82-1.951.90.07310.91071756850.07389.2
1.95-2.112.10.04915.91190255750.04993.9
2.11-2.312.60.0418.41347252150.0495.2
2.31-2.5830.03719.61421947490.03796
2.58-2.983.70.03321.41583742480.03396.9
2.98-3.653.70.02525.91357836410.02597.8
3.65-5.163.70.02227.41041528370.02298.1
5.16-51.7393.60.02523.5566915930.02597.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
AMoREphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
JDirectordata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→51.739 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.01 / SU B: 3.298 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1942 2246 5.1 %RANDOM
Rwork0.1725 ---
obs0.1736 44463 89.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 51.53 Å2 / Biso mean: 14.3049 Å2 / Biso min: 3.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.11 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.63→51.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3058 0 57 395 3510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223223
X-RAY DIFFRACTIONr_bond_other_d0.0010.022117
X-RAY DIFFRACTIONr_angle_refined_deg0.8941.9664382
X-RAY DIFFRACTIONr_angle_other_deg0.72435164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8475390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5124.765170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.7815561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2221524
X-RAY DIFFRACTIONr_chiral_restr0.0570.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023640
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02636
X-RAY DIFFRACTIONr_mcbond_it0.2871.51914
X-RAY DIFFRACTIONr_mcbond_other0.0471.5790
X-RAY DIFFRACTIONr_mcangle_it0.58823118
X-RAY DIFFRACTIONr_scbond_it1.11331309
X-RAY DIFFRACTIONr_scangle_it1.9474.51264
LS refinement shellResolution: 1.631→1.673 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 125 -
Rwork0.195 2516 -
all-2641 -
obs--72.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.40330.00480.1360.3643-0.04260.4791-0.01040.03430.01930.0058-0.02970.0331-0.00410.04950.04010.0068-0.00350.0090.02210.0050.02257.19812.00819.998
20.62390.0610.0580.61620.08540.5165-0.05040.03020.044-0.0449-0.00810.0997-0.02230.0450.05850.0101-0.0054-0.00830.01480.00590.02625.993-12.3172.761
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 230
2X-RAY DIFFRACTION2B20 - 230

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