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- PDB-3bmc: Structure of Pteridine Reductase 1 (PTR1) from Trypanosoma brucei... -

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Basic information

Entry
Database: PDB / ID: 3bmc
TitleStructure of Pteridine Reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and substrate (folate)
Components(Pteridine reductase) x 2
KeywordsOXIDOREDUCTASE / pteridine reductase / ptr1 / trypanosoma brucei / short chain dehydrogenase / substrate / folate
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
FOLIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 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
DepositionDec 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pteridine reductase
B: Pteridine reductase
C: Pteridine reductase
D: Pteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,43412
Polymers122,6954
Non-polymers4,7398
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.441, 88.596, 81.587
Angle α, β, γ (deg.)90.000, 115.340, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: GLU / End label comp-ID: FOL / Refine code: 1 / Auth seq-ID: 2 - 270 / Label seq-ID: 22 - 1

Dom-IDAuth asym-IDLabel asym-ID
1AA - F
2BB - H
3CC - J
4DD - L

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Components

#1: Protein Pteridine reductase /


Mass: 30685.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290
#2: Protein Pteridine reductase /


Mass: 30669.791 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290
#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-FOL / FOLIC ACID / Folate


Mass: 441.397 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H19N7O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 1.98 Å3/Da / Density % sol: 37.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 2-3M sodium acetate, 10-100mM sodium citrate, pH 4.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→73.737 Å / Num. obs: 23556 / % possible obs: 81.1 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 9.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.6-2.742.30.3772709331520.37774
2.74-2.912.20.2712.8710732110.27180.3
2.91-3.112.20.1834.1689431200.18382.7
3.11-3.362.20.1186.4653929440.11884
3.36-3.682.20.0788599127270.07884.1
3.68-4.112.10.05412.7511524350.05483.7
4.11-4.752.10.04114.7449821460.04183.4
4.75-5.812.20.03516.5387117810.03581.4
5.81-8.222.20.0317293713410.0379.5
8.22-37.672.30.02815.616016990.02876.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→37.67 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.91 / SU B: 23.25 / SU ML: 0.249 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.421 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: All of the 17 related structures are expressed from the same DNA construct, which encodes CYS at positions 59 and 168. Crystals harvested within a couple of days of formation contain CYS at ...Details: All of the 17 related structures are expressed from the same DNA construct, which encodes CYS at positions 59 and 168. Crystals harvested within a couple of days of formation contain CYS at positions 59 and 168. However these two residues appear quite reactive and over time become oxidised to CSX, as determined by the emergence in older crystals of electron density for the OD atom. Sometimes CYS168 reacts with DTT in the crystallisation buffer, covalently linking the two molecules by an S-S bond.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1224 5.2 %RANDOM
Rwork0.189 ---
obs0.192 23539 79.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.712 Å2
Baniso -1Baniso -2Baniso -3
1--4.56 Å20 Å2-2.83 Å2
2--7.48 Å20 Å2
3----5.34 Å2
Refinement stepCycle: LAST / Resolution: 2.6→37.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7405 0 320 253 7978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228017
X-RAY DIFFRACTIONr_angle_refined_deg1.462.01310968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.44451032
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99824.434309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.034151272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6181548
X-RAY DIFFRACTIONr_chiral_restr0.0970.21296
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025972
X-RAY DIFFRACTIONr_nbd_refined0.2070.24355
X-RAY DIFFRACTIONr_nbtor_refined0.3030.25580
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2860.2446
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3660.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4180.211
X-RAY DIFFRACTIONr_mcbond_it0.33125182
X-RAY DIFFRACTIONr_mcangle_it0.54838097
X-RAY DIFFRACTIONr_scbond_it0.924.53300
X-RAY DIFFRACTIONr_scangle_it1.23962847
Refine LS restraints NCS

Ens-ID: 1 / Number: 1784 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ATIGHT POSITIONAL0.050.05
2BTIGHT POSITIONAL0.050.05
3CTIGHT POSITIONAL0.040.05
4DTIGHT POSITIONAL0.040.05
1ATIGHT THERMAL0.070.5
2BTIGHT THERMAL0.070.5
3CTIGHT THERMAL0.070.5
4DTIGHT THERMAL0.070.5
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 74 -
Rwork0.316 1485 -
all-1559 -
obs--71.84 %
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)
12.197-0.19270.4421.02420.1211.3182-0.06110.1579-0.0669-0.02970.0012-0.06950.12360.28380.0599-0.02530.0145-0.0007-0.1117-0.0133-0.109211.5872-2.00629.4266
22.46-0.18020.28310.47330.00252.0573-0.01750.26530.0595-0.0717-0.04460.0531-0.0448-0.05420.0621-0.0059-0.0068-0.006-0.17950.0306-0.0799-17.61566.391-1.2581
32.55190.00130.25530.41830.30392.04980.0269-0.20680.14430.15350.0021-0.0764-0.14110.1403-0.0290.01930.0163-0.0342-0.1149-0.0349-0.09021.72428.186637.4767
42.106-0.05520.55240.5816-0.0481.5998-0.072-0.237-0.14640.06550.02950.12540.1197-0.29660.04250.0045-0.01830.0375-0.09390.0266-0.0588-27.5808-0.600827.5796
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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