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- PDB-3jqb: Crystal structure of pteridine reductase 1 (PTR1) from Trypanosom... -

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Basic information

Entry
Database: PDB / ID: 3jqb
TitleCrystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 2-amino-5-(2-phenylethyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one (DX6)
Components(Pteridine reductase ...) x 2
KeywordsOXIDOREDUCTASE / PTERIDINE REDUCTASE / PTR1 / TRYPANOSOMA BRUCEI / SHORT CHAIN DEHYDROGENASE / INHIBITOR
Function / homology
Function and homology information


pteridine reductase / pteridine reductase activity / oxidoreductase activity / nucleotide binding / cytosol
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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Chem-DX6 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTulloch, L.B. / Hunter, W.N.
CitationJournal: J.Med.Chem. / Year: 2010
Title: Structure-based design of pteridine reductase inhibitors targeting african sleeping sickness and the leishmaniases.
Authors: Tulloch, L.B. / Martini, V.P. / Iulek, J. / Huggan, J.K. / Lee, J.H. / Gibson, C.L. / Smith, T.K. / Suckling, C.J. / Hunter, W.N.
History
DepositionSep 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
SupersessionJan 19, 2010ID: 3BMH
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pteridine reductase 1
B: Pteridine reductase 1
C: Pteridine reductase 1
D: Pteridine reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,58612
Polymers122,6954
Non-polymers3,8918
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20140 Å2
ΔGint-134.1 kcal/mol
Surface area32260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.671, 90.433, 82.564
Angle α, β, γ (deg.)90.000, 115.540, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 268
2116B1 - 268
3116C1 - 268
4116D1 - 268

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Components

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Pteridine reductase ... , 2 types, 4 molecules ABDC

#1: Protein Pteridine reductase 1


Mass: 30669.791 Da / Num. of mol.: 3 / Fragment: UNP residues 102-369
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: PTR1, Tb927.8.2210 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q581W1, pteridine reductase
#2: Protein Pteridine reductase 1


Mass: 30685.787 Da / Num. of mol.: 1 / Fragment: UNP residues 102-369
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: PTR1, Tb927.8.2210 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q581W1, pteridine reductase

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Non-polymers , 4 types, 366 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-DX6 / 2-amino-5-(2-phenylethyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one


Mass: 254.287 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H14N4O
#5: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 2-3M Sodium acetate, 10-100mM Sodium citrate, pH 4.0-6.0, VAPOR DIFFUSION, temperature 293K
PH range: 4.0-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 20, 2006
Details: Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.4→45.22 Å / Num. obs: 38283 / % possible obs: 98.7 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.532.60.1294.21440655610.12999.2
2.53-2.682.60.1274.71371353130.12799.3
2.68-2.872.60.11651289149960.11699.4
2.87-3.12.60.0995.61208446620.09999.5
3.1-3.392.60.1024.71105542810.10299.5
3.39-3.792.50.134.3975538710.1399.3
3.79-4.382.40.1214.6795832640.12194.5
4.38-5.372.50.0796.5736628970.07999.1
5.37-7.592.60.0796.2574822510.07999
7.59-45.222.40.0814.9289011870.08194.6

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.21data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2C7V

2c7v


Resolution: 2.4→45.22 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.847 / WRfactor Rfree: 0.291 / WRfactor Rwork: 0.223 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.82 / SU B: 15.877 / SU ML: 0.194 / SU R Cruickshank DPI: 0.657 / SU Rfree: 0.291 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.657 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1952 5.1 %RANDOM
Rwork0.192 ---
obs0.195 38265 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 85.22 Å2 / Biso mean: 7.994 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å20.22 Å2
2--1.66 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7427 0 257 358 8042
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227819
X-RAY DIFFRACTIONr_angle_refined_deg1.0042.00310661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9345992
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69824.305302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.045151236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0591548
X-RAY DIFFRACTIONr_chiral_restr0.060.21262
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025773
X-RAY DIFFRACTIONr_nbd_refined0.1680.23858
X-RAY DIFFRACTIONr_nbtor_refined0.2890.25436
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2533
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.27
X-RAY DIFFRACTIONr_mcbond_it0.79645115
X-RAY DIFFRACTIONr_mcangle_it1.33567935
X-RAY DIFFRACTIONr_scbond_it1.73983108
X-RAY DIFFRACTIONr_scangle_it2.508102721
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1820 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ALOOSE POSITIONAL0.425
BLOOSE POSITIONAL0.45
CLOOSE POSITIONAL0.385
DLOOSE POSITIONAL0.45
ALOOSE THERMAL1.5210
BLOOSE THERMAL1.6310
CLOOSE THERMAL1.8810
DLOOSE THERMAL1.3910
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 144 -
Rwork0.183 2654 -
all-2798 -
obs--99.15 %

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