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- PDB-4cm4: Crystal structure of pteridine reductase 1 (PTR1) from Trypanosom... -

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Basic information

Entry
Database: PDB / ID: 4cm4
TitleCrystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor and inhibitor
Components(PTERIDINE REDUCTASE ...) x 2
KeywordsOXIDOREDUCTASE / PTR1 / 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
Chem-4NR / ACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.81 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)126,85215
Polymers122,6954
Non-polymers4,15711
Water12,935718
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20300 Å2
ΔGint-131.1 kcal/mol
Surface area32740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.673, 89.714, 82.732
Angle α, β, γ (deg.)90.00, 115.68, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.7747, -0.03182, -0.6315), (-0.03747, -0.9947, 0.09609), (-0.6312, 0.0981, 0.7694)-2.253, 3.874, -1.006
2given(0.7712, 0.01676, 0.6363), (0.01831, -0.9998, 0.004146), (0.6363, 0.008454, -0.7714)-13.79, 6.069, 38.1
3given(-0.9999, 0.01168, -0.00426), (0.01205, 0.9947, -0.1018), (0.003048, -0.1018, -0.9948)-15.82, 2.055, 37.62

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Components

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

#1: Protein PTERIDINE REDUCTASE 1 /


Mass: 30685.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290, pteridine reductase
#2: Protein PTERIDINE REDUCTASE 1 /


Mass: 30669.791 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290, pteridine reductase

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Non-polymers , 5 types, 729 molecules

#3: 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
#4: Chemical
ChemComp-4NR / 5-(4-fluorophenyl)-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine


Mass: 243.240 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H10FN5
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 18.015 Da / Num. of mol.: 718 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsS-OXY CYSTEINE (CSX): CYSTEINE 168 MODIFIED TO S-OXY CYSTEINE IN CHAIN A
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: 2.04 Å3/Da / Density % sol: 39.57 % / 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 / Detector: IMAGE PLATE / Date: Sep 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.81→19.76 Å / Num. obs: 83224 / % possible obs: 92.6 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 24.7
Reflection shellResolution: 1.81→1.9 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 8.2 / % possible all: 77.1

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Processing

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

Resolution: 1.81→19.3 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.2 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.113 / 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
Rfree0.18246 4148 5 %RANDOM
Rwork0.14628 ---
obs0.1481 79029 92.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.061 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å2-0.87 Å2
2--3.44 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 1.81→19.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7468 0 278 718 8464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197945
X-RAY DIFFRACTIONr_bond_other_d0.0010.027642
X-RAY DIFFRACTIONr_angle_refined_deg1.6742.00610843
X-RAY DIFFRACTIONr_angle_other_deg0.813.00217502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.81851015
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.36824.267307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.763151264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0251550
X-RAY DIFFRACTIONr_chiral_restr0.0870.21277
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218993
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021781
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_it1.4861.7044026
X-RAY DIFFRACTIONr_mcbond_other1.4831.7034023
X-RAY DIFFRACTIONr_mcangle_it2.4212.5355015
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9651.9863919
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: 1.807→1.854 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 202 -
Rwork0.198 4055 -
obs--64.35 %

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