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- PDB-6rb6: Crystal structure of T. brucei PDE-B1 catalytic domain with inhib... -

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Basic information

Entry
Database: PDB / ID: 6rb6
TitleCrystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-053
ComponentsPhosphodiesterase
KeywordsHYDROLASE / Parasitic phosphodiesterase / African trypanosomiasis / sleeping sickness
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / axoneme / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cell morphogenesis / signal transduction / metal ion binding / cytoplasm
Similarity search - Function
Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / GAF domain / 3'5'-cyclic nucleotide phosphodiesterase / Domain present in phytochromes and cGMP-specific phosphodiesterases. / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. ...Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / GAF domain / 3'5'-cyclic nucleotide phosphodiesterase / Domain present in phytochromes and cGMP-specific phosphodiesterases. / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / GAF domain / GAF-like domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FORMIC ACID / GUANIDINE / Chem-JX2 / Phosphodiesterase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSingh, A.K. / Brown, D.G.
Funding support1items
OrganizationGrant numberCountry
European Union602666
CitationJournal: Bioorg.Med.Chem. / Year: 2019
Title: Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors (Part 2).
Authors: de Heuvel, E. / Singh, A.K. / Boronat, P. / Kooistra, A.J. / van der Meer, T. / Sadek, P. / Blaazer, A.R. / Shaner, N.C. / Bindels, D.S. / Caljon, G. / Maes, L. / Sterk, G.J. / Siderius, M. ...Authors: de Heuvel, E. / Singh, A.K. / Boronat, P. / Kooistra, A.J. / van der Meer, T. / Sadek, P. / Blaazer, A.R. / Shaner, N.C. / Bindels, D.S. / Caljon, G. / Maes, L. / Sterk, G.J. / Siderius, M. / Oberholzer, M. / de Esch, I.J.P. / Brown, D.G. / Leurs, R.
History
DepositionApr 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 4, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphodiesterase
B: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,78531
Polymers81,2472
Non-polymers2,53829
Water7,530418
1
A: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,85815
Polymers40,6231
Non-polymers1,23514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,92616
Polymers40,6231
Non-polymers1,30315
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)147.516, 115.070, 63.780
Angle α, β, γ (deg.)90.00, 109.39, 90.00
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 Phosphodiesterase /


Mass: 40623.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: residues 565-918 / Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: PDEB1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): codon plus
References: UniProt: Q8WQX9, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases

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Non-polymers , 7 types, 447 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-GAI / GUANIDINE / Guanidine


Mass: 59.070 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CH5N3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical ChemComp-JX2 / 3-[5-[(4~{a}~{R},8~{a}~{S})-3-cycloheptyl-4-oxidanylidene-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-yl]-2-methoxy-phenyl]-~{N}-(furan-2-ylmethyl)prop-2-ynamide


Mass: 499.601 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H33N3O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 0.4 M sodium formate, 0.3 M guanidine, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.9→69.57 Å / Num. obs: 78709 / % possible obs: 99.7 % / Redundancy: 3.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.061 / Rrim(I) all: 0.11 / Net I/σ(I): 7.2
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 2 / Num. unique obs: 4518 / CC1/2: 0.475 / Rpim(I) all: 0.405 / Rrim(I) all: 0.748 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I15

4i15


Resolution: 1.9→69.57 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.174 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.107 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1972 3878 4.9 %RANDOM
Rwork0.16547 ---
obs0.16703 74823 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.256 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20 Å2-0.14 Å2
2---1.16 Å20 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 1.9→69.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5272 0 168 418 5858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135545
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175130
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.6437469
X-RAY DIFFRACTIONr_angle_other_deg1.431.57311853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8545668
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.50422.159301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35715938
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2961536
X-RAY DIFFRACTIONr_chiral_restr0.090.2706
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026205
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021185
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7372.9012669
X-RAY DIFFRACTIONr_mcbond_other2.7352.8982668
X-RAY DIFFRACTIONr_mcangle_it3.8934.3313335
X-RAY DIFFRACTIONr_mcangle_other3.8934.3353336
X-RAY DIFFRACTIONr_scbond_it4.0613.412876
X-RAY DIFFRACTIONr_scbond_other4.063.4112877
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1114.9114134
X-RAY DIFFRACTIONr_long_range_B_refined7.90735.3956231
X-RAY DIFFRACTIONr_long_range_B_other7.90635.4056232
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 286 -
Rwork0.297 5544 -
obs--99.79 %

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