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

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Basic information

Entry
Database: PDB / ID: 6rfw
TitleCrystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-1039
ComponentsPhosphodiesterase
KeywordsHYDROLASE / Parasitic phosphodiesterase / African trypanosomiasis / sleeping sickness
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / 3',5'-cyclic-nucleotide phosphodiesterase activity / axoneme / 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 / 3'5'-cyclic nucleotide phosphodiesterase / 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 ...Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase / 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 / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / GAF-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
FORMIC ACID / GUANIDINE / Chem-K1Q / Phosphodiesterase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.183 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 16, 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 / software / 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 / _software.name / _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)82,96016
Polymers81,2472
Non-polymers1,71314
Water4,864270
1
A: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4578
Polymers40,6231
Non-polymers8347
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5038
Polymers40,6231
Non-polymers8807
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.716, 116.553, 68.525
Angle α, β, γ (deg.)90.00, 108.17, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1118-

HOH

21A-1246-

HOH

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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, 284 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH5N3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-K1Q / 3-[5-[(4~{a}~{R},8~{a}~{S})-4-oxidanylidene-3-propan-2-yl-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-yl]-2-methoxy-phenyl]-~{N}-[2-(2-fluorophenyl)ethyl]prop-2-ynamide


Mass: 487.565 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H30FN3O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.66 Å3/Da / Density % sol: 53.76 %
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: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.183→65.11 Å / Num. obs: 42706 / % possible obs: 96.9 % / Redundancy: 3.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.029 / Rrim(I) all: 0.054 / Net I/σ(I): 15.3
Reflection shellResolution: 2.183→2.191 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 462 / CC1/2: 0.889 / Rpim(I) all: 0.369 / Rrim(I) all: 0.682 / % possible all: 97.7

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Processing

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

4i15


Resolution: 2.183→65.11 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.952 / SU B: 8.78 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.196 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 2062 4.8 %RANDOM
Rwork0.17476 ---
obs0.1777 40644 96.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 54.573 Å2
Baniso -1Baniso -2Baniso -3
1-5.07 Å2-0 Å2-1.36 Å2
2--2.12 Å2-0 Å2
3----5.18 Å2
Refinement stepCycle: LAST / Resolution: 2.183→65.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5248 0 113 270 5631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135457
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175045
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.6367376
X-RAY DIFFRACTIONr_angle_other_deg1.3441.57311666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.225662
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79322.297296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1715930
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9821534
X-RAY DIFFRACTIONr_chiral_restr0.0780.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026103
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021171
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_it4.9115.5872654
X-RAY DIFFRACTIONr_mcbond_other4.9035.5852653
X-RAY DIFFRACTIONr_mcangle_it6.9938.3673314
X-RAY DIFFRACTIONr_mcangle_other6.9928.373315
X-RAY DIFFRACTIONr_scbond_it5.2066.0982803
X-RAY DIFFRACTIONr_scbond_other5.2056.12804
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.5668.9324063
X-RAY DIFFRACTIONr_long_range_B_refined9.73466.6366353
X-RAY DIFFRACTIONr_long_range_B_other9.73366.6376354
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.183→2.24 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 157 -
Rwork0.387 3077 -
obs--99.51 %

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