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- PDB-8of2: Trypanosoma brucei pteridine reductase 1 (TbPTR1) in complex with... -

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Basic information

Entry
Database: PDB / ID: 8of2
TitleTrypanosoma brucei pteridine reductase 1 (TbPTR1) in complex with 2,4,6 triamminopyrimidine (TAP)
ComponentsPteridine reductase
KeywordsOXIDOREDUCTASE / Trypanosoma brucei / pteridine reductase / PTR1 / TbPTR1 / triamminopyrimidine
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
PYRIMIDINE-2,4,6-TRIAMINE / ACETATE ION / Chem-NDP / Pteridine reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsTassone, G. / Landi, G. / Mangani, S. / Pozzi, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)603240European Union
CitationJournal: Eur.J.Med.Chem. / Year: 2023
Title: The discovery of aryl-2-nitroethyl triamino pyrimidines as anti-Trypanosoma brucei agents.
Authors: Linciano, P. / Pozzi, C. / Tassone, G. / Landi, G. / Mangani, S. / Santucci, M. / Luciani, R. / Ferrari, S. / Santarem, N. / Tagliazucchi, L. / Cordeiro-da-Silva, A. / Tonelli, M. / Tondi, D. ...Authors: Linciano, P. / Pozzi, C. / Tassone, G. / Landi, G. / Mangani, S. / Santucci, M. / Luciani, R. / Ferrari, S. / Santarem, N. / Tagliazucchi, L. / Cordeiro-da-Silva, A. / Tonelli, M. / Tondi, D. / Bertarini, L. / Gul, S. / Witt, G. / Moraes, C.B. / Costantino, L. / Costi, M.P.
History
DepositionMar 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: 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)126,34215
Polymers122,6794
Non-polymers3,66211
Water19,5461085
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22120 Å2
ΔGint-120 kcal/mol
Surface area31840 Å2
Unit cell
Length a, b, c (Å)74.770, 91.052, 83.027
Angle α, β, γ (deg.)90.00, 115.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Pteridine reductase


Mass: 30669.791 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76290

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Non-polymers , 5 types, 1096 molecules

#2: Chemical
ChemComp-3AY / PYRIMIDINE-2,4,6-TRIAMINE


Mass: 125.132 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H7N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1085 / 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: 2.39 Å3/Da / Density % sol: 48.57 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 26, 2020
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.48→74.86 Å / Num. obs: 161484 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 17.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.036 / Rrim(I) all: 0.074 / Net I/σ(I): 8.6
Reflection shellResolution: 1.48→1.56 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 24272 / CC1/2: 0.831 / Rpim(I) all: 0.337 / Rrim(I) all: 0.678 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→74.86 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.622 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19465 8239 5.1 %RANDOM
Rwork0.16187 ---
obs0.16358 153017 96.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.329 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: 1 / Resolution: 1.48→74.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7409 0 240 1085 8734
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0128082
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.63711082
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05951076
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.89222.39364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.188151282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6161550
X-RAY DIFFRACTIONr_chiral_restr0.1080.21126
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026082
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_it1.8351.9954127
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6772.9775162
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4822.2513955
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.25630.36413269
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: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 548 -
Rwork0.306 11707 -
obs--99.68 %

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