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- PDB-3jq7: Crystal structure of pteridine reductase 1 (PTR1) from Trypanosom... -

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Basic information

Entry
Database: PDB / ID: 3jq7
TitleCrystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 6-phenylpteridine-2,4,7-triamine (DX2)
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 / nucleoplasm / cytoplasm / 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
ACETATE ION / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 6-phenylpteridine-2,4,7-triamine / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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: 3BME
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_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)127,05015
Polymers122,7914
Non-polymers4,25911
Water11,007611
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20490 Å2
ΔGint-137.2 kcal/mol
Surface area31490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.538, 90.029, 82.359
Angle α, β, γ (deg.)90.000, 115.490, 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 ACDB

#1: Protein Pteridine reductase 1


Mass: 30701.787 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 , 5 types, 622 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-DX2 / 6-phenylpteridine-2,4,7-triamine


Mass: 253.263 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H11N7
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 611 / 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: 39.45 %
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: ID23-1 / Wavelength: 1.0064 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0064 Å / Relative weight: 1
ReflectionResolution: 1.8→74.34 Å / Num. obs: 90613 / % possible obs: 99.7 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.92.90.25338767132250.25100
1.9-2.012.90.1455.136184125340.145100
2.01-2.152.90.0917.533693117600.091100
2.15-2.322.80.0639.631081109550.06399.9
2.32-2.552.80.04712.528306100790.04799.8
2.55-2.852.80.03615.22565891140.03699.7
2.85-3.292.70.0314.82200080180.0399.5
3.29-4.022.70.02420.31853468000.02499.4
4.02-5.692.70.02123.31442952970.02199.7
5.69-74.342.80.0219.4797628310.0295.4

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Processing

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

2c7v


Resolution: 1.8→74.33 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.204 / WRfactor Rwork: 0.162 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.879 / SU B: 5.314 / SU ML: 0.08 / SU R Cruickshank DPI: 0.111 / SU Rfree: 0.109 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.191 4569 5 %RANDOM
Rwork0.152 ---
obs0.154 90587 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 81.79 Å2 / Biso mean: 28.332 Å2 / Biso min: 11.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å2-0.79 Å2
2--2.31 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→74.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7338 0 284 611 8233
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227897
X-RAY DIFFRACTIONr_angle_refined_deg1.5012.00910801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56651022
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99524.323303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.115151244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7411548
X-RAY DIFFRACTIONr_chiral_restr0.0920.21281
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025848
X-RAY DIFFRACTIONr_nbd_refined0.2080.24210
X-RAY DIFFRACTIONr_nbtor_refined0.3040.25519
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2674
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3580.215
X-RAY DIFFRACTIONr_mcbond_it2.37445109
X-RAY DIFFRACTIONr_mcangle_it3.25867999
X-RAY DIFFRACTIONr_scbond_it4.69383463
X-RAY DIFFRACTIONr_scangle_it6.029102777
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 1705 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
ALOOSE POSITIONAL0.295
BLOOSE POSITIONAL0.315
CLOOSE POSITIONAL0.355
DLOOSE POSITIONAL0.285
ALOOSE THERMAL2.5910
BLOOSE THERMAL3.0910
CLOOSE THERMAL4.3910
DLOOSE THERMAL2.3210
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 321 -
Rwork0.246 6357 -
all-6678 -
obs--99.94 %
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)
11.22350.04190.13310.67520.02440.8562-0.02180.1264-0.0773-0.0360.0222-0.08770.06780.2538-0.0003-0.07020.020.0079-0.0471-0.0036-0.035611.5907-1.66849.4276
21.2173-0.08830.12750.4792-0.00030.9386-0.01840.22650.0289-0.0674-0.02440.0343-0.0252-0.0830.0428-0.059-0.0026-0.008-0.063-0.0025-0.0639-17.56796.2491-1.3252
31.1444-0.02220.14340.739-0.01671.2307-0.062-0.34280.07690.12230.0268-0.0731-0.04610.09150.0352-0.02610.0094-0.02250.0392-0.0217-0.05151.4667.302537.9722
41.3511-0.21650.18850.66380.11151.0198-0.0396-0.3195-0.150.06160.02560.09040.1035-0.29290.014-0.0648-0.02810.02420.02430.0202-0.0358-27.7446-0.610427.8837
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 268
2X-RAY DIFFRACTION2B2 - 268
3X-RAY DIFFRACTION3C3 - 268
4X-RAY DIFFRACTION4D2 - 268

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