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

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Basic information

Entry
Database: PDB / ID: 3jqg
TitleCrystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 6-[(4-methoxybenzyl)sulfanyl]pyrimidine-2,4-diamine (AX6)
Components(Pteridine reductase 1) 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 / 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
Chem-AX6 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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: 3BMR
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)126,73412
Polymers122,7114
Non-polymers4,0238
Water11,025612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19770 Å2
ΔGint-131.1 kcal/mol
Surface area32150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.531, 89.845, 82.437
Angle α, β, γ (deg.)90.000, 115.530, 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

#1: 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
#2: Protein Pteridine reductase 1


Mass: 30669.791 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: 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-AX6 / 6-[(4-methoxybenzyl)sulfanyl]pyrimidine-2,4-diamine


Mass: 262.331 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H14N4OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 39.4 %
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 225 mm CCD / Detector: CCD / Date: May 20, 2006
Details: Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.9→53.2 Å / Num. obs: 74417 / % possible obs: 96.5 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.092
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 1.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

2c7v


Resolution: 1.9→53.2 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.905 / WRfactor Rfree: 0.272 / WRfactor Rwork: 0.218 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.807 / SU B: 9.514 / SU ML: 0.141 / SU R Cruickshank DPI: 0.195 / SU Rfree: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.267 3738 5 %RANDOM
Rwork0.211 ---
obs0.214 74400 96.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.24 Å2 / Biso mean: 17.855 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--2.9 Å20 Å2-1.19 Å2
2--3.07 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→53.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7406 0 264 612 8282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227862
X-RAY DIFFRACTIONr_angle_refined_deg1.5312.00410722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.951004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04824.257303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.812151248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.361549
X-RAY DIFFRACTIONr_chiral_restr0.0950.21267
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025813
X-RAY DIFFRACTIONr_nbd_refined0.2090.24258
X-RAY DIFFRACTIONr_nbtor_refined0.3020.25422
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2010.2680
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.215
X-RAY DIFFRACTIONr_mcbond_it1.68145117
X-RAY DIFFRACTIONr_mcangle_it2.49767972
X-RAY DIFFRACTIONr_scbond_it3.68783123
X-RAY DIFFRACTIONr_scangle_it4.533102739
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1797 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ALOOSE POSITIONAL0.45
BLOOSE POSITIONAL0.45
CLOOSE POSITIONAL0.375
DLOOSE POSITIONAL0.395
ALOOSE THERMAL3.1410
BLOOSE THERMAL2.9510
CLOOSE THERMAL3.0610
DLOOSE THERMAL2.7310
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 236 -
Rwork0.287 5263 -
all-5499 -
obs--96.39 %
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)
10.7095-0.08320.3110.4922-0.10860.5925-0.00070.1567-0.0383-0.0154-0.0073-0.01230.06950.14640.00800.01280.008-0.0839-0.0059-0.013811.7094-1.70589.6695
20.7811-0.25040.18160.5112-0.04190.6038-0.0090.2174-0.0302-0.022-0.04080.07140.0007-0.01890.0498-0.02520.0001-0.0076-0.0425-0.0118-0.0246-17.50146.1928-1.1161
31.39190.10220.12270.3451-0.07690.6027-0.0569-0.3010.10970.02740.0208-0.055-0.0351-0.04290.03610.00870.0142-0.0064-0.0365-0.0217-0.03421.48327.962638.0749
41.26-0.27720.24120.43870.10540.8527-0.0102-0.2919-0.2075-0.01710.0440.07420.113-0.1988-0.0338-0.0229-0.02210.0249-0.02460.02530.0109-27.815-0.481428.0497
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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