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- PDB-6hnr: Trypanosoma brucei PTR1 in complex with the triazine inhibitor 1 ... -

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Basic information

Entry
Database: PDB / ID: 6hnr
TitleTrypanosoma brucei PTR1 in complex with the triazine inhibitor 1 (F217)
Components(Pteridine reductase) x 2
KeywordsOXIDOREDUCTASE / Trypanosoma brucei / pteridine reductase / PTR1 / TbPTR1 / triazine inhibitors
Function / homology
Function and homology information


pteridine reductase activity / nucleotide binding
Similarity search - Function
Pteridine reductase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-GFE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsLandi, G. / Pozzi, C. / Mangani, S.
Funding support1items
OrganizationGrant numberCountry
European Commission603240
CitationJournal: Acs Infect Dis. / Year: 2019
Title: Structural Insights into the Development of Cycloguanil Derivatives asTrypanosoma bruceiPteridine-Reductase-1 Inhibitors.
Authors: Landi, G. / Linciano, P. / Borsari, C. / Bertolacini, C.P. / Moraes, C.B. / Cordeiro-da-Silva, A. / Gul, S. / Witt, G. / Kuzikov, M. / Costi, M.P. / Pozzi, C. / Mangani, S.
History
DepositionSep 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pteridine reductase
B: Pteridine reductase
C: Pteridine reductase
D: Pteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,04015
Polymers122,7114
Non-polymers4,32811
Water14,034779
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20250 Å2
ΔGint-128 kcal/mol
Surface area31530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.787, 90.449, 82.727
Angle α, β, γ (deg.)90.00, 115.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ADBC

#1: Protein Pteridine reductase


Mass: 30669.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290
#2: Protein Pteridine reductase


Mass: 30685.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290

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Non-polymers , 5 types, 790 molecules

#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-GFE / 1-(3,4-dichlorophenyl)-6,6-dimethyl-1,3,5-triazine-2,4-diamine


Mass: 286.160 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H13Cl2N5
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 779 / 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: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 2-2.5 M sodium acetate, 0.1 M sodium citrate, pH5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 9, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.58→67.49 Å / Num. obs: 131112 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Biso Wilson estimate: 12.2 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.054 / Rrim(I) all: 0.099 / Net I/σ(I): 7.3
Reflection shellResolution: 1.58→1.67 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2 / Num. unique obs: 18783 / CC1/2: 0.842 / Rpim(I) all: 0.326 / Rrim(I) all: 0.582 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JDC

5jdc


Resolution: 1.58→66.32 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.065 / SU ML: 0.069 / SU R Cruickshank DPI: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.089 / SU Rfree Cruickshank DPI: 0.089
RfactorNum. reflection% reflectionSelection details
Rfree0.20872 6573 5 %RANDOM
Rwork0.17191 ---
obs0.17374 124295 96.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.638 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.177 Å
Refinement stepCycle: 1 / Resolution: 1.58→66.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7291 0 278 779 8348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0127919
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0231.66510861
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.925.011043
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.92621.543350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.247151200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3631550
X-RAY DIFFRACTIONr_chiral_restr0.1280.21102
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025989
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.041.7844065
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9022.6545077
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8112.073854
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.50426.6812626
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 456 -
Rwork0.322 9035 -
obs--94.4 %

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