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- PDB-4jep: Crystal structure of Toxoplasma gondii nucleoside triphosphate di... -

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Basic information

Entry
Database: PDB / ID: 4jep
TitleCrystal structure of Toxoplasma gondii nucleoside triphosphate diphosphohydrolase 1 (NTPDase1)
ComponentsNucleoside-triphosphatase 2
KeywordsHYDROLASE / phosphatase / NTPDase
Function / homology
Function and homology information


symbiont-containing vacuole / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase
Similarity search - Function
Nucleotidyltransferase; domain 5 - #530 / Nucleotidyltransferase; domain 5 - #540 / Nucleoside-triphosphatase, alveolata / GDA1/CD39 family of nucleoside phosphatases signature. / Nucleoside phosphatase GDA1/CD39 / GDA1/CD39 (nucleoside phosphatase) family / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoside-triphosphatase 2
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsKrug, U. / Totzauer, R. / Strater, N.
CitationJournal: Proteins / Year: 2013
Title: The crystal structure of Toxoplasma gondii nucleoside triphosphate diphosphohydrolase 1 represents a conformational intermediate in the reductive activation mechanism of the tetrameric enzyme.
Authors: Krug, U. / Totzauer, R. / Strater, N.
History
DepositionFeb 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Dec 25, 2013Group: Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside-triphosphatase 2
B: Nucleoside-triphosphatase 2


Theoretical massNumber of molelcules
Total (without water)136,1522
Polymers136,1522
Non-polymers00
Water0
1
A: Nucleoside-triphosphatase 2
B: Nucleoside-triphosphatase 2

A: Nucleoside-triphosphatase 2
B: Nucleoside-triphosphatase 2


Theoretical massNumber of molelcules
Total (without water)272,3054
Polymers272,3054
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area11870 Å2
ΔGint-67 kcal/mol
Surface area99430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.743, 161.517, 236.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Nucleoside-triphosphatase 2 / / NTPase-II / Nucleoside triphosphate hydrolase 2 / Nucleoside-triphosphatase II


Mass: 68076.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Gene: NTP1 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta pLysS
References: UniProt: Q27895, nucleoside-triphosphate phosphatase

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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: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris pH 8.5, 50 mM MgCl2, 25% (v/v) pentaerythritol propoxylate (17/8 PO/OH), VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 3.1→39.38 Å / Num. obs: 25690 / Biso Wilson estimate: 81.36 Å2

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→36.31 Å / Cor.coef. Fo:Fc: 0.8099 / Cor.coef. Fo:Fc free: 0.7419 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3052 1306 5.09 %RANDOM
Rwork0.2698 ---
obs0.2715 25652 99.38 %-
Displacement parametersBiso mean: 71.12 Å2
Baniso -1Baniso -2Baniso -3
1-5.7566 Å20 Å20 Å2
2---7.536 Å20 Å2
3---1.7795 Å2
Refine analyzeLuzzati coordinate error obs: 0.786 Å
Refinement stepCycle: LAST / Resolution: 3.1→36.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8772 0 0 0 8772
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0078948HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9112109HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3151SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes239HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1291HARMONIC5
X-RAY DIFFRACTIONt_it8948HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion1.39
X-RAY DIFFRACTIONt_other_torsion19.81
X-RAY DIFFRACTIONt_chiral_improper_torsion1155SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact9409SEMIHARMONIC4
LS refinement shellResolution: 3.1→3.23 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2726 138 5.09 %
Rwork0.2405 2571 -
all0.2421 2709 -
obs--99.38 %
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)
100.05830.27780.7658-0.65370-0.004-0.01040.0074-0.00310.0067-0.02240.0222-0.011-0.0027-0.00050.08650.0230.04530.02680.0357-67.9529-19.8844-69.9935
23.4694-1.05550.32841.22480.39081.85780.0412-0.1421-0.00120.04990.0475-0.0495-0.00610.177-0.08860.0798-0.15150.0035-0.3040.04290.1326-29.4719-18.7323-40.5763
30.464-0.84391.45161.44311.33792.9143-0.0081-0.18110.05110.09680.052-0.05030.10120.1367-0.04380.124-0.1520.1208-0.3040.04420.062-31.2695-8.2872-13.133
40.83990.05460.27420-0.0220.0111-0.00110.01550.0066-0.02470.0026-0.0045-0.00950.0038-0.0015-0.045-0.01180.00490.0424-0.03230.0698-31.134237.432-90.1921
52.7598-0.09280.2743.07780.95462.5135-0.026-0.0248-0.2538-0.0217-0.01210.1585-0.13610.02160.0381-0.304-0.05170.0222-0.3040.1380.304-22.187334.5625-44.2226
61.7506-1.03371.83641.9738-1.06541.0971-0.01750.0038-0.20620.234-0.055-0.1074-0.0260.15170.0725-0.304-0.08890.0628-0.2570.1520.304-0.493921.3466-31.3588
70.0130.58170.37220.3608-0.66040.38270.0013-0.02390.00590.0201-0.0060.0143-0.0033-0.01470.00470.0386-0.0095-0.03530.00720.09430.0336-15.857918.8138-15.472
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|33 - A|58}A33 - 58
2X-RAY DIFFRACTION2{A|59 - A|250 A|586 - A|629}A59 - 250
3X-RAY DIFFRACTION2{A|59 - A|250 A|586 - A|629}A586 - 629
4X-RAY DIFFRACTION3{A|271 - A|394 A|425 - A|585}A271 - 394
5X-RAY DIFFRACTION3{A|271 - A|394 A|425 - A|585}A425 - 585
6X-RAY DIFFRACTION4{B|36 - B|58}B36 - 58
7X-RAY DIFFRACTION5{B|59 - B|250 B|586 - B|621}B59 - 250
8X-RAY DIFFRACTION5{B|59 - B|250 B|586 - B|621}B586 - 621
9X-RAY DIFFRACTION6{B|271 - B|394 B|425 - B|585}B271 - 394
10X-RAY DIFFRACTION6{B|271 - B|394 B|425 - B|585}B425 - 585
11X-RAY DIFFRACTION7{B|395 - B|424}B395 - 424

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