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

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Basic information

Entry
Database: PDB / ID: 6fdx
TitleCrystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-1086
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-D5Z / FORMIC ACID / GUANIDINE / Phosphodiesterase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.31 Å
AuthorsSingh, A.K. / Brown, D.G.
CitationJournal: To be published
Title: TbrPDEB1 structure with inhibitor NPD-1086
Authors: Salado, I.G. / Moreno, C. / Sakaine, G. / Singh, A.K. / Blaazer, A.R. / Siderius, M. / Matheeussen, A. / Gul, S. / Maes, L. / Leurs, R. / Brown, D.G. / Augustyns, K.
History
DepositionDec 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 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_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)82,96418
Polymers81,2472
Non-polymers1,71716
Water2,594144
1
A: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4829
Polymers40,6231
Non-polymers8598
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4829
Polymers40,6231
Non-polymers8598
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.102, 116.385, 68.310
Angle α, β, γ (deg.)90.00, 108.67, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1120-

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)
References: UniProt: Q8WQX9, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases

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Non-polymers , 6 types, 160 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-D5Z / (4aS,8aR)-2-[1-(2-aminoquinazolin-4-yl)piperidin-4-yl]-4-(3,4-dimethoxyphenyl)-1,2,4a,5,8,8a-hexahydrophthalazin-1-one


Mass: 512.603 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H32N6O3
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical
ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH5N3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.65 Å3/Da / Density % sol: 53.57 %
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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97622 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 12, 2016 / Details: CRL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.31→57.1 Å / Num. obs: 36029 / % possible obs: 97.1 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.033 / Rrim(I) all: 0.061 / Net I/σ(I): 12.3
Reflection shellResolution: 2.31→2.34 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1815 / CC1/2: 0.91 / Rpim(I) all: 0.312 / Rrim(I) all: 0.592 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
autoPROCdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.31→57.1 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.953 / SU B: 9.738 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.221
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U values refined individually
RfactorNum. reflection% reflectionSelection details
Rfree0.23191 1717 4.8 %RANDOM
Rwork0.16909 ---
obs0.17218 34309 97.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 66.101 Å2
Baniso -1Baniso -2Baniso -3
1-4.58 Å20 Å2-0.71 Å2
2--1.73 Å20 Å2
3----4.74 Å2
Refinement stepCycle: 1 / Resolution: 2.31→57.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5260 0 114 144 5518
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195472
X-RAY DIFFRACTIONr_bond_other_d0.0020.025061
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.9567398
X-RAY DIFFRACTIONr_angle_other_deg1.0322.98311690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82623.84263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.34315933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0351535
X-RAY DIFFRACTIONr_chiral_restr0.0880.2829
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026130
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021181
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_it5.0536.4722658
X-RAY DIFFRACTIONr_mcbond_other5.0526.4732659
X-RAY DIFFRACTIONr_mcangle_it7.3819.6973319
X-RAY DIFFRACTIONr_mcangle_other7.389.6993320
X-RAY DIFFRACTIONr_scbond_it5.3386.9012814
X-RAY DIFFRACTIONr_scbond_other5.3366.8992813
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.92310.1464080
X-RAY DIFFRACTIONr_long_range_B_refined10.49176.8626432
X-RAY DIFFRACTIONr_long_range_B_other10.48576.8636424
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.309→2.369 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 119 -
Rwork0.354 2518 -
obs--97.06 %

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