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- PDB-4a57: CRYSTAL STRUCTURE OF TOXOPLASMA GONDII NUCLEOSIDE TRIPHOSPHATE DI... -

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Basic information

Entry
Database: PDB / ID: 4a57
TitleCRYSTAL STRUCTURE OF TOXOPLASMA GONDII NUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE 3 (NTPDASE3)
ComponentsNUCLEOSIDE-TRIPHOSPHATASE 1
KeywordsHYDROLASE / 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 1
Similarity search - Component
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2 Å
AuthorsKrug, U. / Zebisch, M. / Straeter, N.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Insight Into the Activation Mechanism of Toxoplasma Gondii Nucleoside Triphosphate Diphosphohydrolases by Disulfide Reduction.
Authors: Krug, U. / Zebisch, M. / Krauss, M. / Straeter, N.
History
DepositionOct 24, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Other
Revision 1.2Feb 15, 2012Group: Other
Revision 1.3Dec 25, 2013Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUCLEOSIDE-TRIPHOSPHATASE 1
B: NUCLEOSIDE-TRIPHOSPHATASE 1
C: NUCLEOSIDE-TRIPHOSPHATASE 1
D: NUCLEOSIDE-TRIPHOSPHATASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,7748
Polymers270,6324
Non-polymers1424
Water24,6991371
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16330 Å2
ΔGint-124.3 kcal/mol
Surface area96780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.960, 165.940, 97.510
Angle α, β, γ (deg.)90.00, 97.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NUCLEOSIDE-TRIPHOSPHATASE 1 / / NTPDASE3 / NTPASE-I / NUCLEOSIDE TRIPHOSPHATE HYDROLASE 1 / NUCLEOSIDE-TRIPHOSPHATASE I


Mass: 67657.922 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYSS
References: UniProt: Q27893, nucleoside-triphosphate phosphatase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1371 / 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: 2.64 Å3/Da / Density % sol: 53.88 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2→40.39 Å / Num. obs: 183360 / % possible obs: 97.9 % / Observed criterion σ(I): 2.9 / Redundancy: 5.1 % / Biso Wilson estimate: 25.99 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.9 / % possible all: 97.9

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2→39.43 Å / Cor.coef. Fo:Fc: 0.9444 / Cor.coef. Fo:Fc free: 0.9307 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=19866. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=19866. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=4.
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 1844 1.01 %RANDOM
Rwork0.1741 ---
obs0.1745 183317 --
Displacement parametersBiso mean: 32.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.7943 Å20 Å24.5647 Å2
2---1.2229 Å20 Å2
3----0.5715 Å2
Refine analyzeLuzzati coordinate error obs: 0.227 Å
Refinement stepCycle: LAST / Resolution: 2→39.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18408 0 4 1371 19783
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0118886HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0425593HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6700SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes502HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2754HARMONIC5
X-RAY DIFFRACTIONt_it18886HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion16.06
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2432SEMIHARMONIC5
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_contact22080SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2068 163 1.2 %
Rwork0.1936 13446 -
all0.1938 13609 -
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)
10.232-0.4541-0.96491.3497-1.67150.5355-0.0036-0.13450.06610.01760.02310.0644-0.0263-0.0195-0.0195-0.1348-0.0198-0.00220.17590.025-0.09978.938315.056182.5508
21.1669-0.03940.6480.7259-0.32411.0119-0.1328-0.08490.17880.03610.0213-0.0177-0.1185-0.09330.1115-0.07560.0357-0.0263-0.0482-0.0191-0.0418-4.501526.750939.4406
30.209-0.3068-0.83450.5412-0.6667-0.209-0.00630.0011-0.00280.02160.02220.0028-0.0302-0.0175-0.01590.00770.14260.0945-0.04270.0480.1465-4.0897-12.295341.929
40.5824-0.17320.10230.56390.0170.49930.0243-0.0022-0.05180.0097-0.04670.0539-0.0078-0.01790.0224-0.03620.00660.0081-0.0366-0.012-0.0434-28.184915.014926.2768
52.6925-0.4926-0.39483.14091.00411.81240.04740.0473-0.1081-0.12440.0383-0.2659-0.0820.1568-0.0857-0.00620.0208-0.00150.01880.008-0.0553-14.073318.19678.7761
60.71251.4771-2.00490.90010.4773-0.4907-0.00160.07850.0319-0.0862-0.0326-0.0526-0.02310.14470.0342-0.0866-0.0010.0170.15930.0973-0.120153.1954-20.063239.5245
70.8952-0.26480.63971.2911-0.86551.72080.19960.0538-0.1706-0.1928-0.0070.20010.4250.0755-0.1926-0.04110.0395-0.0861-0.1089-0.0058-0.103311.0371-21.285619.6001
80.0568-0.1876-0.226801.4834-0.05670.0030.02630.00190.01040.03540.02-0.0163-0.0014-0.03840.0464-0.04310.06420.0363-0.1057-0.002619.520416.324426.5355
90.75810.26510.09010.61350.03471.2132-0.04130.0582-0.0539-0.02940.0512-0.04480.01730.0668-0.0099-0.09190.02820.0005-0.05360.0021-0.02894.332-3.7059-2.6249
10-0.21540.3820.76441.48521.17031.7683-0.03490.0630.09220.1335-0.00970.05580.0062-0.08320.0446-0.03540.03310.00960.01110.00210.0186-15.8089-4.55268.4221
110.8128-0.3689-0.32790.0096-0.5387-0.0932-0.0335-0.08540.04820.01840.056-0.01490.1495-0.0373-0.0225-0.0881-0.1152-0.11020.05710.13890.0062-6.8672-28.699232.2435
121.043-0.13850.19360.62830.03341.15950.04890.0738-0.078-0.0785-0.00770.04250.05170.0385-0.0412-0.02960.0083-0.0307-0.09590.0134-0.046632.6978-28.375751.4787
130.48530.81510.30030.664-0.06830.0759-0.0027-0.016-0.0452-0.00680.00010.0147-0.00430.00250.00260.08370.01340.0926-0.14240.08060.16710.029-0.479467.6362
140.75950.10260.34010.5257-0.03550.640.0241-0.0463-0.03310.13-0.0252-0.0073-0.0215-0.04360.0012-0.0155-0.0111-0.009-0.07910.0018-0.04736.2061-28.101180.1912
151.5744-1.133-0.77644.40361.65953.18660.05430.06710.1025-0.15340.0342-0.1478-0.1968-0.1028-0.0885-0.0408-0.0391-0.0378-0.05020.04270.02553.5445-14.729773.5904
160.1367-0.7866-0.30950.3208-0.13050.73240.00280.02090.11420.0529-0.0159-0.03260.07420.01020.0131-0.1292-0.039-0.03370.08350.1205-0.004111.147834.951925.1392
171.7513-0.11250.32450.4557-0.27141.1848-0.0633-0.24590.23470.0469-0.0135-0.0151-0.1215-0.04470.0768-0.07510.0081-0.0178-0.0697-0.0427-0.06824.925723.451565.1857
18-0.0134-0.04820.05350.62470.96390.01340.0012-0.0186-0.0122-0.02180.00050.0039-0.0163-0.0263-0.00170.1035-0.0184-0.0573-0.1005-0.12690.094139.4666-3.299540.015
190.54940.05690.57250.50360.40433.0648-0.07610.06030.00670.00830.0123-0.0177-0.23730.55580.0639-0.1043-0.0308-0.0052-0.0180.043-0.123652.119115.86571.0032
20-0.38371.39271.45651.93531.18821.61160.0104-0.0051-0.11760.018-0.08520.03380.01990.01370.07480.0345-0.0206-0.0309-0.05590.0366-0.002741.57190.835985.0764
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 36- 58)
2X-RAY DIFFRACTION2(CHAIN A AND RESSEQ 59-256, 586-629)
3X-RAY DIFFRACTION3(CHAIN A AND RESSEQ 257-268)
4X-RAY DIFFRACTION4(CHAIN A AND RESSEQ 269-394, 425-585)
5X-RAY DIFFRACTION5(CHAIN A AND RESSEQ 395-424)
6X-RAY DIFFRACTION6(CHAIN B AND RESSEQ 36-58)
7X-RAY DIFFRACTION7(CHAIN B AND RESSEQ 59-256, 586-629)
8X-RAY DIFFRACTION8(CHAIN B AND RESSEQ 257-268)
9X-RAY DIFFRACTION9(CHAIN B AND RESSEQ 269-394, 425-585)
10X-RAY DIFFRACTION10(CHAIN B AND RESSEQ 395-424)
11X-RAY DIFFRACTION11(CHAIN C AND RESSEQ 40-58)
12X-RAY DIFFRACTION12(CHAIN C AND RESSEQ 59-256, 586-629)
13X-RAY DIFFRACTION13(CHAIN C AND RESSEQ 257-268)
14X-RAY DIFFRACTION14CHAIN C AND RESSEQ 269-394,425-585)
15X-RAY DIFFRACTION15(CHAIN C AND RESSEQ 395-424)
16X-RAY DIFFRACTION16(CHAIN D AND RESSEQ 40-58)
17X-RAY DIFFRACTION17(CHAIN D AND RESSEQ 59-256,586-629)
18X-RAY DIFFRACTION18(CHAIN D AND RESSEQ 257-268)
19X-RAY DIFFRACTION19(CHAIN D AND RESSEQ 269-394, 425-585)
20X-RAY DIFFRACTION20(CHAIN D AND RESSEQ 395-424)

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