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- PDB-7a2f: Crystal structure of T. brucei PDE-B1 catalytic domain with inhib... -

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Basic information

Entry
Database: PDB / ID: 7a2f
TitleCrystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-656
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
3'5'-cyclic nucleotide phosphodiesterase / GAF domain / 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. / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain ...3'5'-cyclic nucleotide phosphodiesterase / GAF domain / 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. / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain
Similarity search - Domain/homology
FORMIC ACID / GUANIDINE / Chem-QWZ / Phosphodiesterase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSingh, A.K. / Blaazer, A.R. / Zara, L. / de Esch, I.J.P. / Leurs, R. / Brown, D.G.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)602666European Union
CitationJournal: To be published
Title: Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-656
Authors: Singh, A.K. / Brown, D.G.
History
DepositionAug 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)82,76520
Polymers81,2472
Non-polymers1,51818
Water7,188399
1
A: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,22611
Polymers40,6231
Non-polymers60210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-50 kcal/mol
Surface area15090 Å2
MethodPISA
2
B: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5399
Polymers40,6231
Non-polymers9168
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-48 kcal/mol
Surface area14530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.580, 115.000, 68.450
Angle α, β, γ (deg.)90.000, 108.360, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1165-

HOH

21A-1317-

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, 417 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 / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-GAI / GUANIDINE / Guanidine


Mass: 59.070 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH5N3
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-QWZ / 1-cycloheptyl-3-{4-methoxy-3-[2-(4-methoxyphenyl)ethoxy]phenyl}-4,4-dimethyl-4,5-dihydro-1H-pyrazol-5-one / 2-cycloheptyl-5-[4-methoxy-3-[2-(4-methoxyphenyl)ethoxy]phenyl]-4,4-dimethyl-pyrazol-3-one


Mass: 464.596 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H36N2O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 53.79 %
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: 0.97623 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 28, 2016 / Details: CRL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2→79.38 Å / Num. obs: 54278 / % possible obs: 94.9 % / Redundancy: 2.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.064 / Rrim(I) all: 0.112 / Net I/σ(I): 9.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 2 / Num. unique obs: 4098 / CC1/2: 0.44 / Rpim(I) all: 0.532 / Rrim(I) all: 0.91 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I15

4i15


Resolution: 2→79.38 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.598 / SU ML: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 2601 4.8 %RANDOM
Rwork0.1876 ---
obs0.1893 51676 94.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 125.3 Å2 / Biso mean: 29.834 Å2 / Biso min: 6.31 Å2
Baniso -1Baniso -2Baniso -3
1-4.61 Å2-0 Å2-0.41 Å2
2---1.78 Å2-0 Å2
3----2.09 Å2
Refinement stepCycle: final / Resolution: 2→79.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5260 0 96 399 5755
Biso mean--48 37.39 -
Num. residues----665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135444
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175044
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.6377351
X-RAY DIFFRACTIONr_angle_other_deg1.3511.58311660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6335663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39622.466292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37115933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6831535
X-RAY DIFFRACTIONr_chiral_restr0.0720.2701
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026172
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021165
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 182 -
Rwork0.339 3907 -
all-4089 -
obs--97.03 %

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