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

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Basic information

Entry
Database: PDB / ID: 6ftm
TitleCrystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-048
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 / 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 / GAF-like domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-E6Z / FORMIC ACID / GUANIDINE / Phosphodiesterase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSingh, A.K. / Brown, D.G.
CitationJournal: To be published
Title: Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-048
Authors: de Heuvel, E. / Singh, A.K. / Brown, D.G.
History
DepositionFeb 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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)84,26542
Polymers81,2472
Non-polymers3,01940
Water5,891327
1
A: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,53428
Polymers40,6231
Non-polymers1,91127
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,73114
Polymers40,6231
Non-polymers1,10813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)149.052, 114.730, 63.800
Angle α, β, γ (deg.)90.00, 109.43, 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, 367 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: CH5N3
#6: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical ChemComp-E6Z / 3-{5-[(4aR,8aS)-3-cycloheptyl-4-oxo-3,4,4a,5,8,8a-hexahydrophthalazin-1-yl]-2-methoxyphenyl}prop-2-ynamide


Mass: 419.516 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H29N3O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 3.17 Å3/Da / Density % sol: 61.22 %
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
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: 2.1→70.28 Å / Num. obs: 58838 / % possible obs: 99.8 % / Redundancy: 3.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.069 / Rrim(I) all: 0.125 / Net I/σ(I): 7.1
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4554 / CC1/2: 0.603 / Rpim(I) all: 0.343 / Rrim(I) all: 0.589 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I15

4i15


Resolution: 2.1→70.28 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.945 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.136 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19758 2988 5.1 %RANDOM
Rwork0.15705 ---
obs0.15911 55845 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.055 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å20.21 Å2
2---1.26 Å20 Å2
3---0.18 Å2
Refinement stepCycle: 1 / Resolution: 2.1→70.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5272 0 197 327 5796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195536
X-RAY DIFFRACTIONr_bond_other_d0.0020.025186
X-RAY DIFFRACTIONr_angle_refined_deg1.8341.9657438
X-RAY DIFFRACTIONr_angle_other_deg1.1222.98411947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8265664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53823.893262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3615936
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7291536
X-RAY DIFFRACTIONr_chiral_restr0.1090.2830
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026155
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021231
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_it2.5982.942662
X-RAY DIFFRACTIONr_mcbond_other2.5982.9412663
X-RAY DIFFRACTIONr_mcangle_it3.7134.3873324
X-RAY DIFFRACTIONr_mcangle_other3.7134.3883325
X-RAY DIFFRACTIONr_scbond_it3.8273.3762872
X-RAY DIFFRACTIONr_scbond_other3.8173.3772872
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7544.8754112
X-RAY DIFFRACTIONr_long_range_B_refined7.28435.2516114
X-RAY DIFFRACTIONr_long_range_B_other7.28735.2626115
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 215 -
Rwork0.246 4137 -
obs--99.79 %

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