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- PDB-6tbx: Trypanosoma brucei PTR1 (TbPTR1) in complex with a tricyclic-base... -

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Basic information

Entry
Database: PDB / ID: 6tbx
TitleTrypanosoma brucei PTR1 (TbPTR1) in complex with a tricyclic-based inhibitor
Components(Pteridine reductase) x 2
KeywordsOXIDOREDUCTASE / Trypanosoma brucei / pteridine reductase / TbPTR1 / tricyclic based 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 / 2,4-bis(azanyl)-9~{H}-pyrimido[4,5-b]indol-6-ol / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsLandi, G. / Tassone, G. / Pozzi, C. / Mangani, S.
Funding support1items
OrganizationGrant numberCountry
European Union603240
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: High-resolution crystal structure of Trypanosoma brucei pteridine reductase 1 in complex with an innovative tricyclic-based inhibitor.
Authors: Landi, G. / Linciano, P. / Tassone, G. / Costi, M.P. / Mangani, S. / Pozzi, C.
History
DepositionNov 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
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)126,74015
Polymers122,6954
Non-polymers4,04511
Water13,331740
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20130 Å2
ΔGint-125 kcal/mol
Surface area31350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.677, 90.779, 82.810
Angle α, β, γ (deg.)90.000, 115.650, 90.000
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 /


Mass: 30669.791 Da / Num. of mol.: 3
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
#2: Protein Pteridine reductase /


Mass: 30685.787 Da / Num. of mol.: 1
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, 751 molecules

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


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-N0Z / 2,4-bis(azanyl)-9~{H}-pyrimido[4,5-b]indol-6-ol


Mass: 215.211 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H9N5O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 740 / 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: 2.1 Å3/Da / Density % sol: 41.41 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 2-2.5M sodium acetate, 0.1M sodium citrate, pH 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.3→45.39 Å / Num. obs: 234209 / % possible obs: 96.2 % / Redundancy: 3 % / Biso Wilson estimate: 11.4 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.053 / Rrim(I) all: 0.094 / Net I/σ(I): 8.3
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 33331 / CC1/2: 0.803 / Rpim(I) all: 0.37 / Rrim(I) all: 0.64 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JDC

5jdc


Resolution: 1.3→41.83 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.784 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1594 11767 5 %RANDOM
Rwork0.126 ---
obs0.1277 222393 96.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.97 Å2 / Biso mean: 17.12 Å2 / Biso min: 8.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0 Å2-0.02 Å2
2---0.07 Å2-0 Å2
3---0.08 Å2
Refine analyzeLuzzati coordinate error obs: 0.14 Å
Refinement stepCycle: final / Resolution: 1.3→41.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7230 0 270 749 8249
Biso mean--17.59 33.09 -
Num. residues----986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0137981
X-RAY DIFFRACTIONr_bond_other_d0.0060.0177437
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.67910985
X-RAY DIFFRACTIONr_angle_other_deg1.6631.58317194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24251082
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04222.216334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.029151226
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4271546
X-RAY DIFFRACTIONr_chiral_restr0.0970.21115
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029047
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021609
X-RAY DIFFRACTIONr_rigid_bond_restr6.79336848
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 791 -
Rwork0.211 16167 -
all-16958 -
obs--93.74 %

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