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- PDB-4kh6: Toxoplasma gondii NTPDase1 C258S/C268S E493G crystallized with Mg... -

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Basic information

Entry
Database: PDB / ID: 4kh6
TitleToxoplasma gondii NTPDase1 C258S/C268S E493G crystallized with Mg and AMPNP
ComponentsNucleoside-triphosphatase 2
KeywordsHYDROLASE / Actin-like fold / 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
Chem-AU1 / Nucleoside-triphosphatase 2
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Refined with PDB-ID 4A5B / Resolution: 2.4 Å
AuthorsKrug, U. / Totzauer, R. / Strater, N.
CitationJournal: Chembiochem / Year: 2013
Title: The ATP/ADP substrate specificity switch between Toxoplasma gondii NTPDase1 and NTPDase3 is caused by an altered mode of binding of the substrate base.
Authors: Krug, U. / Totzauer, R. / Zebisch, M. / Strater, N.
History
DepositionApr 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Structure summary
Revision 1.2Aug 20, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)136,8456
Polymers135,9442
Non-polymers9014
Water9,080504
1
A: Nucleoside-triphosphatase 2
B: Nucleoside-triphosphatase 2
hetero molecules

A: Nucleoside-triphosphatase 2
B: Nucleoside-triphosphatase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)273,69012
Polymers271,8884
Non-polymers1,8028
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area17750 Å2
ΔGint-114 kcal/mol
Surface area90520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.710, 150.240, 241.560
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: 67972.016 Da / Num. of mol.: 2 / Mutation: C258S, C268S, E493G
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
#2: Chemical ChemComp-AU1 / 5'-O-[(R)-hydroxy(phosphonoamino)phosphoryl]adenosine / Adenosine 5-(alpha,beta-imido)diphosphate


Mass: 426.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N6O9P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 100 mM Tris (pH 8.8), 50 mM MgCl2, 25% (v/v) pentaerythritol propoxylate (17/8 PO/OH), 10 mM AMPNP, 10 mM magnesium acetate, 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: 2.4→39.19 Å / Num. obs: 52805 / % possible obs: 99.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 45.18 Å2
Reflection shellResolution: 2.4→2.53 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
MAR345data collection
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: Refined with PDB-ID 4A5B / Resolution: 2.4→24.19 Å / Cor.coef. Fo:Fc: 0.9434 / Cor.coef. Fo:Fc free: 0.9147 / SU R Cruickshank DPI: 0.349 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE ELECTRON DENSITY INDICATES BINDING OF THE ADENINE BASE OF AMPNP IN A PUTATIVE TGNTPDASE3 ADP-PRODUCT BINDING MODE. HOWEVER, DUE TO THE WEAK DENSITY THE OCCUPANCY OF THE LIGAND WAS SET TO 0.
RfactorNum. reflection% reflectionSelection details
Rfree0.2131 1083 2.06 %RANDOM
Rwork0.1696 ---
obs0.1705 52612 99.65 %-
Displacement parametersBiso mean: 40.14 Å2
Baniso -1Baniso -2Baniso -3
1--2.8767 Å20 Å20 Å2
2--2.4129 Å20 Å2
3---0.4637 Å2
Refine analyzeLuzzati coordinate error obs: 0.267 Å
Refinement stepCycle: LAST / Resolution: 2.4→24.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9277 0 38 504 9819
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019509HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1612890HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3353SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes251HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1376HARMONIC5
X-RAY DIFFRACTIONt_it9509HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion17.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1227SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10809SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3184 77 2.06 %
Rwork0.2047 3663 -
all0.207 3740 -
obs--99.65 %
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)
10.01540.65042.1941.1754-0.86870.6599-0.03130.1974-0.13560.10420.00110.0631-0.0393-0.06730.0302-0.28610.00970.03150.2915-0.0636-0.0816-6.8968-27.8478-92.8079
21.02950.1021-0.40810.6194-0.18112.1211-0.0552-0.0258-0.1461-0.0232-0.0181-0.0220.23980.10790.0732-0.1061-0.01790.0158-0.08150.0091-0.0237-12.4682-27.8376-45.2115
30.9096-0.85291.40430.28220.41470.90620.00320.02750.01750.0668-0.00610.05840.00360.0150.0029-0.051-0.00260.04260.05860.03910.0189-23.40050.2589-61.6356
40.86210.2979-0.11971.1059-0.28420.6590.0561-0.04560.03180.08480.0050.1614-0.0559-0.0933-0.0611-0.08870.00660.0269-0.04590.0014-0.0122-36.4338-19.904-31.9183
50.066-1.00232.07563.20460.1251.64610.0171-0.20240.03090.1799-0.07660.1081-0.1102-0.0410.05950.0307-0.03370.0144-0.0066-0.0119-0.0785-19.3913-18.13-14.1925
60.7007-2.6726-1.38041.54240.27910-0.0187-0.04910.01310.0020.0033-0.0104-0.08990.14810.0154-0.0788-0.1207-0.02470.29360.0319-0.197730.311614.1253-73.9611
71.1729-0.0355-0.39850.78470.01921.23020.0390.08370.07450.0158-0.0234-0.0075-0.14360.0018-0.0156-0.0365-0.01420.0096-0.1074-0.0062-0.0448-4.879514.2743-41.4037
81.8018-0.19190.333200.40710.5786-0.0225-0.01960.0193-0.0284-0.0129-0.01230.01550.03790.0354-0.0367-0.00380.01230.02790.05170.034914.7488-13.6779-42.7071
90.6341-0.3661-0.29591.13760.20941.91160.0053-0.24030.08540.2680.0891-0.1542-0.36820.4833-0.0943-0.0161-0.0988-0.0058-0.0564-0.0289-0.1426-0.85586.7496-14.4607
100.9563-0.0767-2.71320.5605-2.05341.8375-0.0065-0.1264-0.02760.1615-0.01840.058-0.0222-0.17840.02490.04680.00910.1203-0.0954-0.0171-0.0505-25.45844.7077-17.217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|34 - A|58}A34 - 58
2X-RAY DIFFRACTION2{A|59 - A|256 A|586 - A|629}A59 - 256
3X-RAY DIFFRACTION2{A|59 - A|256 A|586 - A|629}A586 - 629
4X-RAY DIFFRACTION3{A|257 - A|268}A257 - 268
5X-RAY DIFFRACTION4{A|269 - A|394 A|425 - A|585}A269 - 394
6X-RAY DIFFRACTION4{A|269 - A|394 A|425 - A|585}A425 - 585
7X-RAY DIFFRACTION5{A|395 - A|424}A395 - 424
8X-RAY DIFFRACTION6{B|34 - B|58}B34 - 58
9X-RAY DIFFRACTION7{B|59 - B|256 B|586 - B|629}B59 - 256
10X-RAY DIFFRACTION7{B|59 - B|256 B|586 - B|629}B586 - 629
11X-RAY DIFFRACTION8{B|257 - B|268}B257 - 268
12X-RAY DIFFRACTION9{B|269 - B|394 B|425 - B|585}B269 - 394
13X-RAY DIFFRACTION9{B|269 - B|394 B|425 - B|585}B425 - 585
14X-RAY DIFFRACTION10{B|395 - B|424}B395 - 424

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