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- PDB-1e92: Pteridine reductase 1 from Leishmania major complexed with NADP+ ... -

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Basic information

Entry
Database: PDB / ID: 1.0E+92
TitlePteridine reductase 1 from Leishmania major complexed with NADP+ and dihydrobiopterin
ComponentsPTERIDINE REDUCTASE 1
KeywordsPTERIDINE REDUCTASE / TRYPANOSOMATIDS / DRUG RESISTANCE / PTERIN SALVAGE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE
Function / homology
Function and homology information


pteridine reductase / 6,7-dihydropteridine reductase activity / pteridine reductase activity / tetrahydrobiopterin biosynthetic process / response to methotrexate / oxidoreductase activity / 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
7,8-DIHYDROBIOPTERIN / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / : / Pteridine reductase 1
Similarity search - Component
Biological speciesLEISHMANIA MAJOR (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSchuettelkopf, A.W. / Hunter, W.N.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Pteridine Reductase Mechanism Correlates Pterin Metabolism with Drug Resistance in Trypanosomatid Parasites
Authors: Gourley, D.G. / Schuettelkopf, A.W. / Leonard, G.A. / Luba, J. / Hardy, L.W. / Beverley, S.M. / Hunter, W.N.
History
DepositionOct 4, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)125,94116
Polymers121,7624
Non-polymers4,17912
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)94.338, 103.801, 137.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99996, 0.00708, -0.00523), (0.0068, 0.99863, 0.05192), (0.00559, 0.05188, -0.99864)23.12407, -3.62229, 136.56796
2given(-0.80097, -0.01444, 0.59853), (-0.01509, -0.9989, -0.04429), (0.59852, -0.04451, 0.79987)-20.0007, 95.562, 9.02167
3given(0.79984, 0.0107, -0.60011), (0.00995, -0.99994, -0.00456), (-0.60013, -0.00232, -0.7999)43.47491, 92.50438, 132.29491

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Components

#1: Protein
PTERIDINE REDUCTASE 1 / / PTR1


Mass: 30440.580 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Gene: PTR1 / Plasmid: PET 15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: TrEMBL: Q9U1F8, UniProt: Q01782*PLUS, EC: 1.1.1.253
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-HBI / 7,8-DIHYDROBIOPTERIN / Dihydrobiopterin


Mass: 239.231 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H13N5O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 293 K / pH: 5.4
Details: 15 MG/ML PROTEIN, 0.1M NAAC/HAC BUFFER PH 5.5, 12% MPEG 5000, 0.075M CAAC2, 293K
Crystal grow
*PLUS
Temperature: 293 K / pH: 7 / Method: vapor diffusion, sitting drop
Details: Gourley, D.G., (1999) Acta Crystallogr., D55, 1608.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMTris-HCl1drop
21 mMmethotrexate1drop
31 mMNADPH1drop
420 mMdithiothreitol1drop
520 mg/mlprotein1drop
611-14 %PEG50001reservoir
7100 mMsodium acetate1reservoir
8100 mMcalcium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9326
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9326 Å / Relative weight: 1
ReflectionResolution: 2.2→27.74 Å / Num. obs: 62471 / % possible obs: 91.1 % / Redundancy: 2.4 % / Biso Wilson estimate: 25.3 Å2 / Rsym value: 0.077 / Net I/σ(I): 18.9
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 6.7 / Rsym value: 0.198 / % possible all: 84.5
Reflection
*PLUS
Num. measured all: 449654 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
Rmerge(I) obs: 0.198

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E7W

1e7w


Resolution: 2.2→27.77 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2824839.6 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE SIDE CHAIN OF ARG A20 WAS MODELLED WITH TWO ALTERNATE CONFORMATIONS, EACH OF HALF OCCUPANCY. FOR THE SIDE CHAIN ATOMS (OTHER THAN CB) OF RESIDUES A122, A133, A136, A168, C120, C121, ...Details: THE SIDE CHAIN OF ARG A20 WAS MODELLED WITH TWO ALTERNATE CONFORMATIONS, EACH OF HALF OCCUPANCY. FOR THE SIDE CHAIN ATOMS (OTHER THAN CB) OF RESIDUES A122, A133, A136, A168, C120, C121, C132, C133, C137, D120, D168 THE OCCUPANCY VALUES WERE SET TO 0.00 DUE TO LACK OF INTERPRETABLE DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3161 5.1 %RANDOM
Rwork0.198 ---
obs0.198 62471 90.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.0631 Å2 / ksol: 0.341437 e/Å3
Displacement parametersBiso mean: 23.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20 Å20 Å2
2--0.34 Å20 Å2
3----1.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati sigma a0.16 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 2.2→27.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7806 0 276 434 8516
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.741.5
X-RAY DIFFRACTIONc_mcangle_it2.492
X-RAY DIFFRACTIONc_scbond_it2.622
X-RAY DIFFRACTIONc_scangle_it3.442.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 491 5.1 %
Rwork0.2 9103 -
obs--84.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3HET.PARAMHET.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.04
LS refinement shell
*PLUS
Rfactor Rwork: 0.2

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