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- PDB-5jcx: Trypanosoma brucei PTR1 in complex with inhibitor NP-29 -

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Basic information

Entry
Database: PDB / ID: 5jcx
TitleTrypanosoma brucei PTR1 in complex with inhibitor NP-29
ComponentsPteridine reductase
KeywordsOXIDOREDUCTASE / Trypanosoma brucei / pteridine reductase / oxydoreductase / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-CC6 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsLandi, G. / Pozzi, C. / Di Pisa, F. / Dello Iacono, L. / Mangani, S.
Funding support1items
OrganizationGrant numberCountry
European Commission603240
CitationJournal: J.Med.Chem. / Year: 2016
Title: Profiling of Flavonol Derivatives for the Development of Antitrypanosomatidic Drugs.
Authors: Borsari, C. / Luciani, R. / Pozzi, C. / Poehner, I. / Henrich, S. / Trande, M. / Cordeiro-da-Silva, A. / Santarem, N. / Baptista, C. / Tait, A. / Di Pisa, F. / Dello Iacono, L. / Landi, G. / ...Authors: Borsari, C. / Luciani, R. / Pozzi, C. / Poehner, I. / Henrich, S. / Trande, M. / Cordeiro-da-Silva, A. / Santarem, N. / Baptista, C. / Tait, A. / Di Pisa, F. / Dello Iacono, L. / Landi, G. / Gul, S. / Wolf, M. / Kuzikov, M. / Ellinger, B. / Reinshagen, J. / Witt, G. / Gribbon, P. / Kohler, M. / Keminer, O. / Behrens, B. / Costantino, L. / Tejera Nevado, P. / Bifeld, E. / Eick, J. / Clos, J. / Torrado, J. / Jimenez-Anton, M.D. / Corral, M.J. / Alunda, J.M. / Pellati, F. / Wade, R.C. / Ferrari, S. / Mangani, S. / Costi, M.P.
History
DepositionApr 15, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)126,21916
Polymers122,7434
Non-polymers3,47612
Water11,962664
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19590 Å2
ΔGint-129 kcal/mol
Surface area31420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.680, 89.730, 82.840
Angle α, β, γ (deg.)90.00, 115.71, 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: 30685.787 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, 676 molecules

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


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-CC6 / 3,5,7-trihydroxy-2-(2-hydroxyphenyl)-4H-1-benzopyran-4-one


Mass: 286.236 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H10O6
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 664 / 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: 1.93 Å3/Da / Density % sol: 36.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein solution: 8 g/L in 20 mM Tris-HCl pH 7.5, 10 mM DTT; crystallization buffer: 0.1 M sodium citrate pH 5, 2.25 M sodium acetate
PH range: 5.0-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.43→41.77 Å / Num. obs: 171130 / % possible obs: 94.5 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 9.2
Reflection shellResolution: 1.43→1.51 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X9G

2x9g


Resolution: 1.43→37.33 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / Rfactor Rfree error: 0.046 / SU B: 2.79 / SU ML: 0.046 / SU R Cruickshank DPI: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.06 / SU Rfree Cruickshank DPI: 0.06
RfactorNum. reflection% reflectionSelection details
Rfree0.17953 8611 5 %RANDOM
Rwork0.14423 ---
obs0.14604 162483 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.037 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.03 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.43→37.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7214 0 233 664 8111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0197776
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.99510670
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46451046
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11924.57291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.012151198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2951541
X-RAY DIFFRACTIONr_chiral_restr0.0840.21283
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215824
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_it2.1944004
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6654995
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4443772
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.63113074
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.36337194
X-RAY DIFFRACTIONr_sphericity_free32.9885220
X-RAY DIFFRACTIONr_sphericity_bonded12.67757554
LS refinement shellResolution: 1.43→1.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 642 -
Rwork0.328 12023 -
obs--94.84 %

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