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- PDB-4clo: Crystal structure of pteridine reductase 1 (PTR1) from Trypanosom... -

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Basic information

Entry
Database: PDB / ID: 4clo
TitleCrystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor and inhibitor
Components(PTERIDINE REDUCTASE ...) x 2
KeywordsOXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE
Function / homology
Function and homology information


pteridine reductase activity / nucleotide binding
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-XP0 / Pteridine reductase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.88 Å
AuthorsBarrack, K.L. / Hunter, W.N.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Structure-Based Design and Synthesis of Antiparasitic Pyrrolopyrimidines Targeting Pteridine Reductase 1.
Authors: Khalaf, A.I. / Huggan, J.K. / Suckling, C.J. / Gibson, C.L. / Stewart, K. / Giordani, F. / Barrett, M.P. / Wong, P.E. / Barrack, K.L. / Hunter, W.N.
History
DepositionJan 15, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release

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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)126,99013
Polymers122,7114
Non-polymers4,2799
Water14,034779
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23130 Å2
ΔGint-148.6 kcal/mol
Surface area32390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.124, 89.243, 84.382
Angle α, β, γ (deg.)90.00, 115.27, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.7808, -0.02763, 0.6242), (-0.03463, -0.9956, -0.08738), (0.6238, -0.08984, 0.7764)3.497, 1.911, -1.116
2given(0.779, 0.04241, -0.6256), (0.0379, -0.9991, -0.02055), (-0.6259, -0.007704, -0.7799)13.99, 0.09587, 39.56
3given(-1, -0.003862, -0.001744), (-0.004009, 0.9956, 0.09406), (0.001373, 0.09407, -0.9956)17.43, -1.82, 38.36

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Components

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PTERIDINE REDUCTASE ... , 2 types, 4 molecules ADBC

#1: Protein PTERIDINE REDUCTASE 1


Mass: 30669.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290, pteridine reductase
#2: Protein PTERIDINE REDUCTASE 1


Mass: 30685.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290, pteridine reductase

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Non-polymers , 4 types, 788 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-XP0 / 5-(phenylethynyl)-4-(pyrrolidin-1-yl)-7H-pyrrolo[2,3-d]pyrimidin-2-amine


Mass: 303.361 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H17N5
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 779 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsS-OXY CYSTEINE (CSX): CYSTEINE MODIFIED TO S-OXY CYSTEINE IN CHAINS B AND C.
Sequence detailsSEQUENCE CONTAINS ADDITIONAL 20 AMINO ACID HISTIDINE TAG AT N-TERMINUS.

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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: 2.06 Å3/Da / Density % sol: 40.2 % / Description: NONE
Crystal growDetails: RESERVOIR CONTAINED 1.7-2.7 M SODIUM ACETATE, 20-50 MM SODIUM CITRATE PH 4.5-5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU R-AXIS IV IMAGING PLATE / Date: Jun 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.88→19.72 Å / Num. obs: 75665 / % possible obs: 94 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.5
Reflection shellResolution: 1.88→1.98 Å / Redundancy: 4 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 6.6 / % possible all: 81.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.88→19.73 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.102 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES WITH INSUFFICIENT ELECTRON DENSITY WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.20354 3772 5 %RANDOM
Rwork0.15682 ---
obs0.15918 71641 93.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.613 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å2-0.31 Å2
2--3.11 Å20 Å2
3----1.48 Å2
Refinement stepCycle: LAST / Resolution: 1.88→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7470 0 290 779 8539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0198008
X-RAY DIFFRACTIONr_bond_other_d0.0020.027708
X-RAY DIFFRACTIONr_angle_refined_deg1.7142.00910944
X-RAY DIFFRACTIONr_angle_other_deg0.8583.00317677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85551030
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59324.387310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.036151269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1811549
X-RAY DIFFRACTIONr_chiral_restr0.090.21291
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219083
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021786
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5921.7694043
X-RAY DIFFRACTIONr_mcbond_other1.5921.7694042
X-RAY DIFFRACTIONr_mcangle_it2.4972.6335044
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9782.0423965
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.881→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 171 -
Rwork0.287 3865 -
obs--68.76 %

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