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- PDB-5k6a: Trypanosoma brucei Pteridine reductase 1 (PTR1) in complex with c... -

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Basic information

Entry
Database: PDB / ID: 5k6a
TitleTrypanosoma brucei Pteridine reductase 1 (PTR1) in complex with compound 1
Components(Pteridine reductase) x 2
KeywordsOXIDOREDUCTASE / Trypanosoma brucei / pteridine reductase
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
Chem-6QT / ACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLandi, G. / Pozzi, C. / Di Pisa, F. / Dello lacono, L. / Mangani, S.
CitationJournal: Molecules / Year: 2017
Title: Chroman-4-One Derivatives Targeting Pteridine Reductase 1 and Showing Anti-Parasitic Activity.
Authors: Di Pisa, F. / Landi, G. / Dello Iacono, L. / Pozzi, C. / Borsari, C. / Ferrari, S. / Santucci, M. / Santarem, N. / Cordeiro-da-Silva, A. / Moraes, C.B. / Alcantara, L.M. / Fontana, V. / ...Authors: Di Pisa, F. / Landi, G. / Dello Iacono, L. / Pozzi, C. / Borsari, C. / Ferrari, S. / Santucci, M. / Santarem, N. / Cordeiro-da-Silva, A. / Moraes, C.B. / Alcantara, L.M. / Fontana, V. / Freitas-Junior, L.H. / Gul, S. / Kuzikov, M. / Behrens, B. / Pohner, I. / Wade, R.C. / Costi, M.P. / Mangani, S.
History
DepositionMay 24, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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)126,90814
Polymers122,7914
Non-polymers4,11710
Water13,926773
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20070 Å2
ΔGint-130 kcal/mol
Surface area30470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.720, 89.894, 82.684
Angle α, β, γ (deg.)90.00, 115.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ABDC

#1: Protein Pteridine reductase / Pteridine reductase 1


Mass: 30685.787 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76290
#2: Protein Pteridine reductase / Pteridine reductase 1


Mass: 30733.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76290

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Non-polymers , 4 types, 783 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-6QT / (2~{R})-2-(3-hydroxyphenyl)-6-oxidanyl-2,3-dihydrochromen-4-one


Mass: 256.253 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C15H12O4
#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.: 773 / 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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: Protein solution: 6 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 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.999 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 5, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 1.7→74.47 Å / Num. obs: 95660 / % possible obs: 92.66 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Biso Wilson estimate: 8.864 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 6.7
Reflection shellResolution: 1.7→1.742 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 1.8 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3gn1

3gn1


Resolution: 1.7→74.47 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.999 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 4859 4.8 %RANDOM
Rwork0.17962 ---
obs0.18154 95660 92.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.612 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→74.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7210 0 276 773 8259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0197777
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8832.00710665
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.175.0441028
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37924.39287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.769151181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4281543
X-RAY DIFFRACTIONr_chiral_restr0.120.21277
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215811
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_it1.4651.6333981
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2122.4324970
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8291.8463796
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.10625.06313277
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: 1.698→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 365 -
Rwork0.301 6902 -
obs--91.37 %

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