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

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Basic information

Entry
Database: PDB / ID: 3jqa
TitleCrystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 2-amino-1,9-dihydro-6H-purine-6-thione (DX4)
Components(Pteridine reductase ...) x 3
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 / nucleoplasm / cytosol / cytoplasm
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-amino-1,9-dihydro-6H-purine-6-thione / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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: 3BMG
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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)126,38612
Polymers122,7434
Non-polymers3,6428
Water11,494638
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19800 Å2
ΔGint-131.9 kcal/mol
Surface area32820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.997, 90.834, 82.640
Angle α, β, γ (deg.)90.000, 115.500, 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 ... , 3 types, 4 molecules ABCD

#1: Protein Pteridine reductase 1


Mass: 30669.791 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
#2: Protein Pteridine reductase 1


Mass: 30685.787 Da / Num. of mol.: 2 / 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
#3: Protein Pteridine reductase 1


Mass: 30701.787 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 , 3 types, 646 molecules

#4: 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
#5: Chemical
ChemComp-DX4 / 2-amino-1,9-dihydro-6H-purine-6-thione


Mass: 167.192 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5N5S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / 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: 2.07 Å3/Da / Density % sol: 40.58 %
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 21, 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: 1.9→57.64 Å / Num. obs: 78741 / % possible obs: 99.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-23.30.322.137751114330.3299.9
2-2.123.20.2053.234503108440.20599.9
2.12-2.273.10.1424.531317102430.142100
2.27-2.452.90.1035.62798394860.103100
2.45-2.692.80.0777.22475187470.077100
2.69-32.80.0539.12186879050.053100
3-3.472.70.0396.51903469990.039100
3.47-4.252.70.02916.71622259360.029100
4.25-6.012.90.02615.31315746130.026100
6.01-57.642.80.0287716925350.02898.3

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.17data scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2C7V

2c7v


Resolution: 1.9→57.64 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.2 / WRfactor Rwork: 0.157 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.902 / SU B: 5.582 / SU ML: 0.083 / SU R Cruickshank DPI: 0.128 / SU Rfree: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.189 3960 5 %RANDOM
Rwork0.147 ---
obs0.149 78702 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 88.34 Å2 / Biso mean: 23.802 Å2 / Biso min: 6.32 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å20 Å2-0.54 Å2
2--1.63 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 1.9→57.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7414 0 236 638 8288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0227940
X-RAY DIFFRACTIONr_bond_other_d0.0010.025123
X-RAY DIFFRACTIONr_angle_refined_deg1.3422.00310866
X-RAY DIFFRACTIONr_angle_other_deg0.937312606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56651041
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7324.379306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.448151278
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7811548
X-RAY DIFFRACTIONr_chiral_restr0.0730.21294
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028796
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021464
X-RAY DIFFRACTIONr_nbd_refined0.1960.21569
X-RAY DIFFRACTIONr_nbd_other0.1820.25354
X-RAY DIFFRACTIONr_nbtor_refined0.1680.23843
X-RAY DIFFRACTIONr_nbtor_other0.0840.23819
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2468
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0210.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.220
X-RAY DIFFRACTIONr_mcbond_it2.41846554
X-RAY DIFFRACTIONr_mcbond_other0.63842044
X-RAY DIFFRACTIONr_mcangle_it2.82868098
X-RAY DIFFRACTIONr_scbond_it4.0583327
X-RAY DIFFRACTIONr_scangle_it5.252102738
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2957 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ALOOSE POSITIONAL0.455
BLOOSE POSITIONAL0.425
CLOOSE POSITIONAL0.395
DLOOSE POSITIONAL0.445
ALOOSE THERMAL1.9110
BLOOSE THERMAL1.8810
CLOOSE THERMAL2.5710
DLOOSE THERMAL1.6810
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 273 -
Rwork0.189 5504 -
all-5777 -
obs--99.83 %
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)
10.82970.0340.23340.77860.02590.95990.00480.1163-0.064-0.02820.0051-0.0690.09260.233-0.0099-0.05970.02570.0092-0.0353-0.008-0.035811.5952-2.01779.351
21.0011-0.05050.18310.51590.04571.0698-0.01520.1460.043-0.0251-0.02430.0436-0.0465-0.05920.0395-0.05150.004-0.0153-0.0829-0.005-0.05-17.47416.4719-1.3483
31.09980.01930.09670.76430.15251.2498-0.0407-0.16710.09920.05640.0246-0.0253-0.07220.08260.0161-0.02890.0054-0.0147-0.0496-0.0095-0.05171.3938.164738.0038
41.0852-0.13260.18690.64950.13951.0905-0.0176-0.1667-0.14440.04520.00760.0850.1087-0.22150.0099-0.0508-0.0250.02-0.03260.0066-0.013-27.8324-0.657728.0606
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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