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- PDB-8rhv: Crystal Structure of Trypanosoma brucei PTR1 in complex with the ... -

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Basic information

Entry
Database: PDB / ID: 8rhv
TitleCrystal Structure of Trypanosoma brucei PTR1 in complex with the cofactor and inhibitor P30
ComponentsPteridine reductase
KeywordsOXIDOREDUCTASE / Trypanosoma brucei / PTR1 / Pteridine reductase / cofactor / NADPH / inhibitor
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 domain superfamily
Similarity search - Domain/homology
: / ACETATE ION / Chem-NDP / Pteridine reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPozzi, C. / Mangani, S. / Landi, G.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)CA21111European Union
CitationJournal: Acs Infect Dis. / Year: 2024
Title: Identification of Innovative Folate Inhibitors Leveraging the Amino Dihydrotriazine Motif from Cycloguanil for Their Potential as Anti- Trypanosoma brucei Agents.
Authors: Francesconi, V. / Rizzo, M. / Pozzi, C. / Tagliazucchi, L. / Konchie Simo, C.U. / Saporito, G. / Landi, G. / Mangani, S. / Carbone, A. / Schenone, S. / Santarem, N. / Tavares, J. / Cordeiro- ...Authors: Francesconi, V. / Rizzo, M. / Pozzi, C. / Tagliazucchi, L. / Konchie Simo, C.U. / Saporito, G. / Landi, G. / Mangani, S. / Carbone, A. / Schenone, S. / Santarem, N. / Tavares, J. / Cordeiro-da-Silva, A. / Costi, M.P. / Tonelli, M.
History
DepositionDec 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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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)127,09914
Polymers123,2044
Non-polymers3,89510
Water10,160564
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20200 Å2
ΔGint-130 kcal/mol
Surface area31700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.523, 89.451, 82.632
Angle α, β, γ (deg.)90.00, 115.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pteridine reductase


Mass: 30800.982 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Plasmid: plasmid / Details (production host): pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76290
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-A1H0U / 7-methoxy-4,4-dimethyl-10~{H}-[1,3,5]triazino[1,2-a]benzimidazol-2-amine


Mass: 245.280 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H15N5O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.92 Å3/Da / Density % sol: 36.04 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.6-2.5 M sodium acetate and 0.1 M sodium citrate, pH 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 13, 2023
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 1.7→89.45 Å / Num. obs: 106873 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 27.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.024 / Rrim(I) all: 0.042 / Net I/σ(I): 18.2
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 2 / Num. unique obs: 5251 / CC1/2: 0.808 / Rpim(I) all: 0.483 / Rrim(I) all: 0.851 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→74.73 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.058 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2212 5445 5.1 %RANDOM
Rwork0.18157 ---
obs0.18361 101395 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.023 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: 1 / Resolution: 1.7→74.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7334 0 258 564 8156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0127781
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8731.80910644
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41951007
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.002563
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.883101178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1360.21280
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025758
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_it3.0653.1324001
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.0865.5974982
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5873.3683780
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.07535.2112355
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 383 -
Rwork0.362 7444 -
obs--98.33 %

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