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- PDB-4bae: Optimisation of pyrroleamides as mycobacterial GyrB ATPase inhibi... -

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Basic information

Entry
Database: PDB / ID: 4bae
TitleOptimisation of pyrroleamides as mycobacterial GyrB ATPase inhibitors: Structure Activity Relationship and in vivo efficacy in the mouse model of tuberculosis
ComponentsDNA GYRASE SUBUNIT B
KeywordsISOMERASE / DNA TOPOISOMERASE / INHIBITOR
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
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 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-RWX / DNA gyrase subunit B
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsRead, J.A. / Gingell, H.G. / Madhavapeddi, P.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2014
Title: Optimization of Pyrrolamides as Mycobacterial Gyrb ATPase Inhibitors: Structure Activity Relationship and in Vivo Efficacy in the Mouse Model of Tuberculosis.
Authors: Hameed, S.P. / Solapure, S. / Mukherjee, K. / Nandi, V. / Waterson, D. / Shandil, R. / Balganesh, M. / Sambandamurthy, V.K. / Raichurkar, A.K. / Deshpande, A. / Ghosh, A. / Awasthy, D. / ...Authors: Hameed, S.P. / Solapure, S. / Mukherjee, K. / Nandi, V. / Waterson, D. / Shandil, R. / Balganesh, M. / Sambandamurthy, V.K. / Raichurkar, A.K. / Deshpande, A. / Ghosh, A. / Awasthy, D. / Shanbhag, G. / Sheikh, G. / Mcmiken, H. / Puttur, J. / Reddy, J. / Werngren, J. / Read, J. / Kumar, M. / Manjunatha, R. / Chinnapattu, M. / Madhavapeddi, P. / Manjrekar, P. / Basu, R. / Gaonkar, S. / Sharma, S. / Hoffner, S. / Humnabadkar, V. / Subbulakshmi, V. / Panduga, V.
History
DepositionSep 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Dec 14, 2016Group: Database references
Revision 1.3Nov 8, 2017Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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
C: DNA GYRASE SUBUNIT B
D: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,88216
Polymers91,1024
Non-polymers2,78012
Water2,684149
1
A: DNA GYRASE SUBUNIT B
B: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9017
Polymers45,5512
Non-polymers1,3505
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-19.7 kcal/mol
Surface area19350 Å2
MethodPQS
2
C: DNA GYRASE SUBUNIT B
D: DNA GYRASE SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9819
Polymers45,5512
Non-polymers1,4307
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-7.1 kcal/mol
Surface area19810 Å2
MethodPQS
Unit cell
Length a, b, c (Å)59.191, 78.249, 89.750
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.5585, 0.82947, 0.00742), (0.8295, 0.5585, 0.00276), (-0.00186, 0.0077, -0.99997)
Vector: -19.27874, -16.43661, 142.69847)

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Components

#1: Protein
DNA GYRASE SUBUNIT B


Mass: 22775.564 Da / Num. of mol.: 4 / Fragment: ATPASE DOMAIN, RESIDUES 19-255 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: RESIDUES 213-246 REPLACED BY DG / Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0C559, EC: 5.99.1.3
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-RWX / 2-[(3S,4R)-4-[(3-bromanyl-4-chloranyl-5-methyl-1H-pyrrol-2-yl)carbonylamino]-3-methoxy-piperidin-1-yl]-4-(2-methyl-1,2,4-triazol-3-yl)-1,3-thiazole-5-carboxylic acid


Mass: 558.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H21BrClN7O4S
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsL19M AND RESIDUES 213-246 REPLACED BY DG TO IMPROVE CRYTALLISABILITY

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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: 2.54 Å3/Da / Density % sol: 51.26 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.35→89.8 Å / Num. obs: 32685 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 49.63 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.6
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.8 / % possible all: 91.6

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
MOSFLMdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B6C

4b6c


Resolution: 2.35→59.19 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.9364 / SU R Cruickshank DPI: 0.365 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.35 / SU Rfree Blow DPI: 0.233 / SU Rfree Cruickshank DPI: 0.239
RfactorNum. reflection% reflectionSelection details
Rfree0.2372 1638 5.01 %RANDOM
Rwork0.1942 ---
obs0.1964 32684 95.21 %-
Displacement parametersBiso mean: 62.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.1981 Å20 Å22.0742 Å2
2--12.5795 Å20 Å2
3----12.7776 Å2
Refine analyzeLuzzati coordinate error obs: 0.432 Å
Refinement stepCycle: LAST / Resolution: 2.35→59.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5532 0 156 149 5837
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015802HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.157908HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1874SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes899HARMONIC5
X-RAY DIFFRACTIONt_it5802HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.52
X-RAY DIFFRACTIONt_other_torsion18.46
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion765SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6408SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.43 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2657 139 4.98 %
Rwork0.2188 2654 -
all0.2211 2793 -
obs--95.21 %
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)
12.3005-0.68640.05167.2903-0.05880.7304-0.01390.2629-0.0464-0.459-0.06620.45840.037-0.05420.0801-0.2713-0.01880.0042-0.22720.00320.26262.9472-5.1491-5.1204
22.1948-0.1133-0.12836.3321-0.0051.0609-0.06490.17160.0001-0.28410.0807-0.2682-0.02450.0561-0.0159-0.2586-0.03380.0336-0.2109-0.00820.287626.8710.3668-5.1222
32.4756-0.33960.02877.32570.22190.6972-0.01090.27260.0145-0.5122-0.0246-0.39310.00020.07310.0355-0.304-0.02110.0397-0.27050.00020.30426.76245.158639.7446
41.9814-0.2738-0.0356.519-0.4730.8561-0.07210.2085-0.0381-0.37240.06690.32360.0512-0.06940.0052-0.304-0.03280.0011-0.24340.00230.3042.7098-10.313639.6074
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D

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