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- PDB-4phl: TbrPDEB1-inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 4phl
TitleTbrPDEB1-inhibitor complex
ComponentsClass 1 phosphodiesterase PDEB1
KeywordsHydrolase/Hydrolase Inhibitor / phosphodiesterase / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / cGMP catabolic process / axoneme / 3',5'-cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / cAMP-mediated signaling / cell morphogenesis / 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 / 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. ...Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ETHANOL / GUANIDINE / Chem-PIL / Phosphodiesterase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsChoy, M.S. / Bland, N. / Peti, W. / Page, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: TbrPDEB1-inhibitor complex
Authors: Bland, N. / Choy, M.S. / Pollastri, M. / Campbell, R. / Peti, W. / Page, R.
History
DepositionMay 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 23, 2022Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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
Revision 1.5Sep 27, 2023Group: 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: Class 1 phosphodiesterase PDEB1
B: Class 1 phosphodiesterase PDEB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,32711
Polymers78,1872
Non-polymers1,1399
Water8,233457
1
A: Class 1 phosphodiesterase PDEB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7166
Polymers39,0941
Non-polymers6225
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Class 1 phosphodiesterase PDEB1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6115
Polymers39,0941
Non-polymers5174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.195, 119.265, 68.144
Angle α, β, γ (deg.)90.00, 106.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1127-

HOH

21B-1107-

HOH

31B-1141-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Class 1 phosphodiesterase PDEB1


Mass: 39093.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: PDEB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WQX9

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Non-polymers , 7 types, 466 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-PIL / 3-(CYCLOPENTYLOXY)-N-(3,5-DICHLOROPYRIDIN-4-YL)-4-METHOXYBENZAMIDE / PICLAMILAST


Mass: 381.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18Cl2N2O3 / Comment: antiinflammatory, inhibitor*YM
#5: Chemical ChemComp-GAI / GUANIDINE


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1 M MES, 0.2 M guanidine, 0.4 M sodium formate and 16% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 59427 / % possible obs: 97 % / Redundancy: 7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.9
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.034 / Mean I/σ(I) obs: 3.6 / % possible all: 71.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-3000phasing
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4I15

4i15


Resolution: 1.95→30.962 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1924 3003 5.06 %Random
Rwork0.1597 ---
obs0.1614 59394 96.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→30.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5188 0 67 457 5712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125427
X-RAY DIFFRACTIONf_angle_d1.1377324
X-RAY DIFFRACTIONf_dihedral_angle_d13.7831974
X-RAY DIFFRACTIONf_chiral_restr0.049827
X-RAY DIFFRACTIONf_plane_restr0.006946
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.98110.25211170.20651943X-RAY DIFFRACTION71
1.9811-2.01530.25251140.1872189X-RAY DIFFRACTION80
2.0153-2.05190.19941260.1742454X-RAY DIFFRACTION88
2.0519-2.09140.2181330.16942676X-RAY DIFFRACTION97
2.0914-2.13410.20651450.16092763X-RAY DIFFRACTION100
2.1341-2.18040.21341620.16252757X-RAY DIFFRACTION100
2.1804-2.23120.23111490.16362754X-RAY DIFFRACTION100
2.2312-2.28690.18141510.16222735X-RAY DIFFRACTION100
2.2869-2.34870.22451550.16372788X-RAY DIFFRACTION100
2.3487-2.41780.20771350.16752768X-RAY DIFFRACTION100
2.4178-2.49580.17691300.16882792X-RAY DIFFRACTION100
2.4958-2.5850.19731690.17052743X-RAY DIFFRACTION100
2.585-2.68840.20551340.17062768X-RAY DIFFRACTION100
2.6884-2.81070.22691380.16832790X-RAY DIFFRACTION100
2.8107-2.95880.21591540.19022758X-RAY DIFFRACTION100
2.9588-3.1440.19651480.18212769X-RAY DIFFRACTION100
3.144-3.38650.24621460.17552784X-RAY DIFFRACTION100
3.3865-3.72680.17711540.14832758X-RAY DIFFRACTION100
3.7268-4.26490.17021270.14472818X-RAY DIFFRACTION100
4.2649-5.36870.15651660.1332755X-RAY DIFFRACTION100
5.3687-30.96620.1541500.14272829X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7052-0.2607-0.41041.0220.79081.7731-0.05420.0258-0.0195-0.02270.06480.06550.08410.0633-0.00040.1638-0.0114-0.01130.20220.02560.153125.929437.211731.6512
20.6718-0.2731-0.08361.4691-0.00381.0494-0.0250.0008-0.0250.1105-0.00580.1207-0.0492-0.1197-0.00220.14740.00370.00720.14880.02360.17698.000361.401463.5174
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 587 through 916 )
2X-RAY DIFFRACTION2chain 'B' and (resid 587 through 918 )

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