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

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Basic information

Entry
Database: PDB / ID: 3jqc
TitleCrystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 2-amino-6-bromo-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile (JU2)
ComponentsPteridine reductase 1
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
Chem-JU2 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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: 3BMI
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / 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_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_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

Downloads & links

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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)126,66912
Polymers122,6794
Non-polymers3,9908
Water13,169731
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19740 Å2
ΔGint-131.9 kcal/mol
Surface area32260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.862, 89.114, 84.246
Angle α, β, γ (deg.)90.000, 116.080, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A1 - 204
2113B1 - 204
3113C1 - 204
4113D1 - 204
1213A225 - 270
2213B225 - 270
3213C225 - 270
4213D225 - 270
1123A205 - 224
2123D205 - 224

NCS ensembles :
ID
1
2

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Components

#1: Protein
Pteridine reductase 1


Mass: 30669.791 Da / Num. of mol.: 4 / 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: 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
#3: Chemical
ChemComp-JU2 / 2-amino-6-bromo-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile


Mass: 254.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H4BrN5O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 731 / 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: 2.03 Å3/Da / Density % sol: 39.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: 2-3M Sodium acetate, 10-100mM Sodium citrate, pH 5.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.97897 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 20, 2006
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97897 Å / Relative weight: 1
ReflectionResolution: 1.8→27.65 Å / Num. obs: 84262 / % possible obs: 92.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 11.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.92.70.37722355786040.37765.2
1.9-2.0130.2343.133256111800.23489.6
2.01-2.153.20.1445.337527115680.14498.8
2.15-2.323.20.0928.334685108330.09299
2.32-2.553.20.06511.531702100050.06599.2
2.55-2.8530.04316.92747090280.04399.4
2.85-3.2930.02723.42398280200.02799.6
3.29-4.022.90.0227.81958367890.0299.7
4.02-5.692.80.01826.11483653000.01899.9
5.69-27.652.70.01525.4802029350.01599

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.17data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2C7V

2c7v


Resolution: 1.8→27.65 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.159 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.869 / SU B: 5.902 / SU ML: 0.092 / SU R Cruickshank DPI: 0.136 / SU Rfree: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.204 4262 5.1 %RANDOM
Rwork0.168 79975 --
obs0.17 84237 92.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 71.88 Å2 / Biso mean: 18.318 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--2.12 Å20 Å2-1.05 Å2
2--2.55 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7428 0 248 731 8407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227964
X-RAY DIFFRACTIONr_angle_refined_deg1.4242.00210890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.58351030
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7124.267307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.915151273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9151550
X-RAY DIFFRACTIONr_chiral_restr0.0760.21290
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025906
X-RAY DIFFRACTIONr_nbd_refined0.1930.24478
X-RAY DIFFRACTIONr_nbtor_refined0.2950.25506
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2793
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.227
X-RAY DIFFRACTIONr_mcbond_it1.75165194
X-RAY DIFFRACTIONr_mcangle_it2.51498120
X-RAY DIFFRACTIONr_scbond_it4.272123194
X-RAY DIFFRACTIONr_scangle_it5.387152754
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A888TIGHT POSITIONAL0.030.05
1B888TIGHT POSITIONAL0.040.05
1C888TIGHT POSITIONAL0.030.05
1D888TIGHT POSITIONAL0.030.05
1A761LOOSE POSITIONAL0.615
1B761LOOSE POSITIONAL0.415
1C761LOOSE POSITIONAL0.525
1D761LOOSE POSITIONAL0.415
1A888TIGHT THERMAL0.080.5
1B888TIGHT THERMAL0.080.5
1C888TIGHT THERMAL0.080.5
1D888TIGHT THERMAL0.080.5
1A761LOOSE THERMAL2.6410
1B761LOOSE THERMAL2.4710
1C761LOOSE THERMAL2.4810
1D761LOOSE THERMAL2.6310
2A80TIGHT POSITIONAL0.030.05
2A82LOOSE POSITIONAL0.835
2A80TIGHT THERMAL0.130.5
2A82LOOSE THERMAL3.8810
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 194 -
Rwork0.303 3845 -
all-4039 -
obs--60.46 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.31850.07490.14350.4293-0.01460.3671-0.00970.09930.011-0.0229-0.0051-0.03070.0240.11360.0148-0.03150.01530.00730.00560.0138-0.020311.5282-1.66649.4717
20.4170.0555-0.08860.12270.05540.6838-0.00010.08940.02870.0020.01530.02110.0178-0.0584-0.0152-0.02170.0017-0.0096-0.02630.0145-0.017-17.73116.0502-0.893
30.547-0.02820.18040.1407-0.18650.5474-0.0381-0.06360.02470.02420.0331-0.0164-0.03520.04940.005-0.00250.0004-0.0063-0.0417-0.0057-0.01861.77088.041837.8194
40.6582-0.07280.24810.1144-0.05070.6560-0.0542-0.0520.02590.0310.02050.0665-0.1248-0.031-0.0148-0.01320.0092-0.02880.0128-0.0021-27.5708-0.355928.3349
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 268
2X-RAY DIFFRACTION2B2 - 268
3X-RAY DIFFRACTION3C2 - 268
4X-RAY DIFFRACTION4D2 - 268

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