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

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Basic information

Entry
Database: PDB / ID: 6qgu
TitleCrystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-1361
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-863 / FORMIC ACID / GUANIDINE / Phosphodiesterase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsSingh, A.K. / Blaazer, A.R. / Zara, L. / de Esch, I.J.P. / Leurs, R. / Brown, D.G.
Funding support1items
OrganizationGrant numberCountry
European Union602666
CitationJournal: To be published
Title: Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-1361
Authors: Singh, A.K. / Brown, D.G.
History
DepositionJan 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 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)82,45417
Polymers81,2472
Non-polymers1,20815
Water8,611478
1
A: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,15310
Polymers40,6231
Non-polymers5309
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3017
Polymers40,6231
Non-polymers6776
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.467, 114.814, 68.314
Angle α, β, γ (deg.)90.00, 108.23, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1167-

HOH

21A-1358-

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, 493 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.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-GAI / GUANIDINE


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-863 / 5-(3-(cyclopentyloxy)-4-methoxyphenyl)-2-isopropyl-4,4-dimethyl-2,4-dihydro-3H-pyrazol-3-one


Mass: 344.448 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28N2O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 53.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 0.4 M sodium formate, 0.3 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: 0.97622 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: 1.77→57.4 Å / Num. obs: 80974 / % possible obs: 98.6 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.035 / Rrim(I) all: 0.066 / Net I/σ(I): 12.1
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4092 / CC1/2: 0.741 / Rpim(I) all: 0.397 / Rrim(I) all: 0.734 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I15

4i15


Resolution: 1.77→57.4 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.03 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.097 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19521 4012 5 %RANDOM
Rwork0.15948 ---
obs0.16124 76961 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 32.441 Å2
Baniso -1Baniso -2Baniso -3
1-3.16 Å2-0 Å2-0.44 Å2
2---0.9 Å2-0 Å2
3----1.62 Å2
Refinement stepCycle: 1 / Resolution: 1.77→57.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5260 0 74 478 5812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135424
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175033
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.6357328
X-RAY DIFFRACTIONr_angle_other_deg1.4761.57311639
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5515663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66122.381294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25415933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5331535
X-RAY DIFFRACTIONr_chiral_restr0.0880.2699
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026063
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021162
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_it2.7443.1522658
X-RAY DIFFRACTIONr_mcbond_other2.743.152657
X-RAY DIFFRACTIONr_mcangle_it3.7784.7113319
X-RAY DIFFRACTIONr_mcangle_other3.7784.7143320
X-RAY DIFFRACTIONr_scbond_it4.0983.6292765
X-RAY DIFFRACTIONr_scbond_other4.0983.6312766
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0555.2494010
X-RAY DIFFRACTIONr_long_range_B_refined7.40939.1076533
X-RAY DIFFRACTIONr_long_range_B_other7.438.9646495
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 279 -
Rwork0.32 5742 -
obs--99.75 %

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