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- PDB-4kh4: Toxoplasma gondii NTPDase1 C258S/C268S in complex with Mg and AMPPNP -

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Basic information

Entry
Database: PDB / ID: 4kh4
TitleToxoplasma gondii NTPDase1 C258S/C268S in complex with Mg and AMPPNP
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Nucleoside-triphosphatase 2
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Refined with Refmac, PDB-ID 4A5B / Resolution: 3 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 / 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)137,1496
Polymers136,0882
Non-polymers1,0614
Water0
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)274,29812
Polymers272,1764
Non-polymers2,1228
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area21040 Å2
ΔGint-131 kcal/mol
Surface area88110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.156, 148.267, 242.176
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: 68044.078 Da / Num. of mol.: 2 / Mutation: C258S, C268S
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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 2.45 Å3/Da / Density % sol: 49.71 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 100 mM Tris (pH 8.2), 50 mM MgCl2, 23% (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: 3→39.12 Å / Num. obs: 27204 / % possible obs: 99.8 % / Biso Wilson estimate: 74 Å2
Reflection shellResolution: 3→3.16 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
MAR345data collection
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: Refined with Refmac, PDB-ID 4A5B
Resolution: 3→38.94 Å / Cor.coef. Fo:Fc: 0.8953 / Cor.coef. Fo:Fc free: 0.8676 / Cross valid method: THROUGHOUT / σ(F): 0
Details: AN ADDITIONAL ALTERNATIVE CONFORMATION OF THE ADENINE BASE OF AMPPNP APPEARS POSSIBLE BASED ON THE 3.0 A ELECTRON DENSITY MAPS. THE DENSITY SUGGESTS THAT AMPPNP WITH AN OCCUPANCY OF 0.8 ...Details: AN ADDITIONAL ALTERNATIVE CONFORMATION OF THE ADENINE BASE OF AMPPNP APPEARS POSSIBLE BASED ON THE 3.0 A ELECTRON DENSITY MAPS. THE DENSITY SUGGESTS THAT AMPPNP WITH AN OCCUPANCY OF 0.8 REPRESENTS THE PREDOMINANT BINDING MODE, BUT AN ADDITIONAL ALTERNATIVE BINDING MODE CANNOT BE EXCLUDED ON THE BASIS OF THE LIMITED RESOLUTION OF 3.0 A AND WAS SET TO AN OCCUPANCY OF 0.
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 1364 5.02 %RANDOM
Rwork0.2024 ---
obs0.2039 27166 99.78 %-
Displacement parametersBiso mean: 56.53 Å2
Baniso -1Baniso -2Baniso -3
1--3.2143 Å20 Å20 Å2
2--11.7361 Å20 Å2
3----8.5218 Å2
Refine analyzeLuzzati coordinate error obs: 0.449 Å
Refinement stepCycle: LAST / Resolution: 3→38.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9249 0 46 0 9295
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0079522HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9612917HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3363SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes252HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1399HARMONIC5
X-RAY DIFFRACTIONt_it9522HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.8
X-RAY DIFFRACTIONt_other_torsion19.02
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_contact10521SEMIHARMONIC4
LS refinement shellResolution: 3→3.11 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2856 141 5.03 %
Rwork0.2481 2663 -
all0.25 2804 -
obs--99.78 %
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)
10.72090.7584-0.90030.4466-0.7790.4160.00190.0347-0.01890.0087-0.0117-0.0090.0082-0.00390.0097-0.084-0.0898-0.00760.124-0.04550.0417-7.2104-27.8578-92.2086
20.96540.054-0.14351.1827-0.3413.3161-0.0499-0.0563-0.21290.0301-0.01480.01340.1287-0.00890.0648-0.10.00130.0235-0.05260.0188-0.0405-12.2721-27.3058-45.2929
30.01410.29390.598201.10110.0035-0.0003-0.00230.0164-0.01390.00920.0305-0.0388-0.0331-0.0089-0.04850.14360.0110.0238-0.05660.0424-23.18480.9602-61.5915
41.68141.2809-0.33672.5665-0.39181.26120.0418-0.01270.39240.36640.13440.4924-0.0863-0.1804-0.1762-0.0940.14860.1475-0.05730.0448-0.0797-35.806-19.101-31.938
500.5266-2.02530.4181-0.00181.00680.0015-0.0415-0.01020.0518-0.04310.0183-0.0281-0.02720.04160.22010.02170.0754-0.0463-0.066-0.0986-18.7006-17.6496-14.2689
60.355-0.42351.28050.1330.33061.0211-0.00850.00490.00720.0069-0.0097-0.0087-0.01380.05130.0182-0.0055-0.1362-0.0040.0704-0.0457-0.021828.725414.4013-73.7238
72.6517-0.2161-0.79211.80550.25381.3404-0.0546-0.03230.01860.02940.0688-0.0318-0.53440.049-0.01420.11980.0740.0192-0.1275-0.0264-0.219-4.573714.6399-41.5344
80.98850.0687-0.94470.14270.06320-0.0046-0.03920.00920.01040.0019-0.01230.03040.01640.0027-0.02590.0072-0.01110.0086-0.01530.074115.0728-13.3297-43.0293
90.7093-0.2374-0.1781.43710.36812.3214-0.0204-0.1418-0.1350.48310.0764-0.187-0.23950.2439-0.05610.30320.01630.0379-0.17860.0102-0.3006-0.17127.0435-14.6153
100.0678-0.555-2.08870.79310.79030.90080.0031-0.0026-0.00560.047-0.005-0.0153-0.0127-0.02490.00190.20610.08030.1465-0.0666-0.0784-0.0594-24.86015.0731-17.1824
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|35 - A|58}A35 - 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|37 - B|58}B37 - 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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