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- PDB-5h2r: Crystal structure of T brucei phosphodiesterase B2 bound to compo... -

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Basic information

Entry
Database: PDB / ID: 5h2r
TitleCrystal structure of T brucei phosphodiesterase B2 bound to compound 15b
ComponentsPhosphodiesterase
KeywordsHYDROLASE / Phosphodiesterase Inhibitor Trypanosoma brucei
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / axoneme / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP-mediated signaling / 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-LLN / Phosphodiesterase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNoble, C.G.
CitationJournal: To Be Published
Title: Trypanosomal Phosphodiesterase B1 and B2 as a Potential Therapy for Human African Trypanosomiasis
Authors: Ng, P.S. / Noble, C.G. / Ng, F.S.B. / Chew, S.H. / Lim, C.C. / Manoharan, V. / Wan, K.F. / Vachaspati, P. / Kaiser, M. / Ma, N.L. / Gedeck, P. / Kounde, C. / Rao, S.P.S.
History
DepositionOct 17, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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

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Assembly

Deposited unit
A: Phosphodiesterase
B: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2108
Polymers77,0102
Non-polymers1,2016
Water11,944663
1
A: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1054
Polymers38,5051
Non-polymers6003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1054
Polymers38,5051
Non-polymers6003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.756, 97.756, 120.783
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Phosphodiesterase


Mass: 38504.910 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Strain: 927/4 GUTat10.1
References: UniProt: Q38F42, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#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-LLN / (4~{a}~{S},8~{a}~{R})-2-cycloheptyl-4-[4-(2-hydroxyethyloxy)-3-[2-(2-oxidanylideneimidazolidin-1-yl)ethoxy]phenyl]-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-one


Mass: 510.625 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H38N4O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 663 / 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: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 15-20% PEG 3350, 0.1 M MES, pH 5.5, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→49.16 Å / Num. obs: 61560 / % possible obs: 98.4 % / Redundancy: 10.1 % / Biso Wilson estimate: 20.53 Å2 / Net I/σ(I): 11.8
Reflection shellResolution: 1.8→1.86 Å

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H2Q

5h2q


Resolution: 1.8→49.16 Å / Cor.coef. Fo:Fc: 0.9394 / Cor.coef. Fo:Fc free: 0.9126 / SU R Cruickshank DPI: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.137 / SU Rfree Blow DPI: 0.131 / SU Rfree Cruickshank DPI: 0.127
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 3118 5.1 %RANDOM
Rwork0.1756 ---
obs0.178 61111 98.09 %-
Displacement parametersBiso mean: 23.03 Å2
Baniso -1Baniso -2Baniso -3
1--1.728 Å20 Å20 Å2
2---1.728 Å20 Å2
3---3.4561 Å2
Refine analyzeLuzzati coordinate error obs: 0.194 Å
Refinement stepCycle: 1 / Resolution: 1.8→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5284 0 78 663 6025
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015470HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.987395HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1990SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes150HARMONIC2
X-RAY DIFFRACTIONt_gen_planes787HARMONIC5
X-RAY DIFFRACTIONt_it5470HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.68
X-RAY DIFFRACTIONt_other_torsion17.79
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion694SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7086SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2971 233 5.29 %
Rwork0.2233 4174 -
all0.2271 4407 -
obs--98.09 %

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