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- PDB-4a59: Crystal structure of Toxoplasma gondii nucleoside triphosphate di... -

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Basic information

Entry
Database: PDB / ID: 4a59
TitleCrystal structure of Toxoplasma gondii nucleoside triphosphate diphosphohydrolase 3 (NTPDase3) in complex with AMP
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
ADENOSINE MONOPHOSPHATE / Nucleoside-triphosphatase 1
Similarity search - Component
Biological speciesTOXOPLASMA GONDII (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 18, 2012Group: Other
Revision 1.2Feb 15, 2012Group: Other
Revision 1.3Dec 25, 2013Group: Structure summary
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)272,3689
Polymers270,6324
Non-polymers1,7365
Water15,925884
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17480 Å2
ΔGint-69.1 kcal/mol
Surface area97410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.170, 166.030, 97.940
Angle α, β, γ (deg.)90.00, 97.15, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.148347, -0.182129, 0.97202), (-0.171908, -0.963182, -0.206709), (0.973879, -0.197763, 0.111575)-25.7277, 12.32325, 22.635
2given(0.058623, 0.569961, -0.819578), (0.539846, -0.708689, -0.454231), (-0.83972, -0.415817, -0.349237)51.73873, 12.45954, 73.40094
3given(-0.934217, -0.338744, -0.11176), (-0.334881, 0.724997, 0.601858), (-0.12285, 0.599693, -0.790744)33.89645, -21.48132, 80.75194

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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, apyrase
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 884 / 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: 53.52 % / 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: 2.2→43.4 Å / Num. obs: 142618 / % possible obs: 96.9 % / Observed criterion σ(I): 2.9 / Redundancy: 3 % / Biso Wilson estimate: 37.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.6
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 2 / % possible all: 93.3

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A57

4a57


Resolution: 2.2→42.3 Å / Cor.coef. Fo:Fc: 0.9433 / Cor.coef. Fo:Fc free: 0.9244 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 1399 0.98 %RANDOM
Rwork0.1797 ---
obs0.1802 142579 --
Displacement parametersBiso mean: 41.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.617 Å20 Å22.5628 Å2
2---2.4929 Å20 Å2
3---0.8758 Å2
Refine analyzeLuzzati coordinate error obs: 0.284 Å
Refinement stepCycle: LAST / Resolution: 2.2→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18381 0 115 884 19380
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0118997HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1425764HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6732SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes520HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2768HARMONIC5
X-RAY DIFFRACTIONt_it18997HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion17.53
X-RAY DIFFRACTIONt_improper_torsion20HARMONIC0
X-RAY DIFFRACTIONt_chiral_improper_torsion2427SEMIHARMONIC5
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_contact21623SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2965 100 0.96 %
Rwork0.2121 10366 -
all0.2129 10466 -
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)
10.2879-1.9014-1.12932.0589-3.1717-0.2879-0.0379-0.28430.1835-0.12120.06310.09680.0015-0.0845-0.0253-0.1668-0.0511-0.02830.22170.05-0.08799.173414.957982.2599
21.559-0.0170.45860.9854-0.27551.1646-0.0506-0.06440.1397-0.0315-0.0120.0501-0.1578-0.09210.0626-0.07110.0339-0.0423-0.09190.0004-0.0757-4.736226.608939.8057
30.2380.1453-0.93370.24530.2022-0.238-0.0080.0030.00290.02230.00840.0033-0.023-0.0013-0.0004-0.00640.09960.06830.00310.05560.2169-4.4828-12.372641.7553
40.7608-0.03430.11160.6941-0.0320.57510.04780.0528-0.1284-0.0359-0.0472-0.0068-0.0173-0.0302-0.0007-0.03030.015-0.0174-0.0524-0.0217-0.0614-28.485815.013326.8398
52.8149-1.4027-0.1593.6760.11371.87090.00980.0704-0.0896-0.12040.0067-0.1471-0.05960.2193-0.01650.02880.03990.00850.06050.0075-0.1018-14.306917.99979.0499
61.27782.9321-1.53150.97020.0089-0.3291-0.01250.08070.0556-0.2310.0664-0.08720.00420.2175-0.0538-0.1129-0.01230.05260.1360.0813-0.116353.18-19.796839.9815
71.4882-0.44210.80031.4796-1.43662.16950.23960.1311-0.3379-0.35770.02930.29250.54660.1591-0.2689-0.02840.0792-0.1442-0.1765-0.0201-0.111.2459-21.080119.3666
80.24760.1236-0.991100.17260.0694-0.0038-0.01040.0076-0.00970.0098-0.01560.01420.0075-0.0060.0792-0.05190.07790.0562-0.0167-0.040719.398916.484827.1843
91.35120.39990.19091.0240.15121.7208-0.10460.1161-0.1214-0.0620.1086-0.01810.07440.0481-0.004-0.10680.02580.0104-0.14180.0038-0.04624.2139-3.6908-2.4612
102.3366-0.0878-1.82702.8744-0.49510.0044-0.070.12990.0434-0.01790.00660.0595-0.05840.01350.08040.13650.1602-0.05490.13290.0542-17.4673-5.25427.3708
112.0972-2.584-1.05470.8114-2.7841-0.2947-0.0307-0.08620.0640.05180.0417-0.05010.1249-0.0034-0.0109-0.1427-0.0934-0.18950.01970.14150.1175-6.7694-28.953631.5894
121.3234-0.25350.01260.7315-0.0641.14840.06530.0783-0.0688-0.0221-0.02260.03580.03780.0124-0.0427-0.03470.0063-0.0277-0.11230.0177-0.042532.4243-28.324351.7532
130.19011.0346-0.74570.57050.5283-0.19010.0139-0.0034-0.023-0.0138-0.00120.0079-0.04810.0329-0.01260.0164-0.00920.091-0.06180.10830.19099.9485-0.468868.1333
140.94170.0740.30370.8301-0.08280.97220.0373-0.04960.00270.2433-0.0223-0.0793-0.1032-0.0184-0.0150.0252-0.0593-0.0285-0.1185-0.0111-0.102635.8562-28.251380.2791
152.9449-1.4546-2.41951.39121.85370.1440.05620.19860.2517-0.05090.0795-0.0893-0.0961-0.0459-0.1357-0.0976-0.0783-0.07860.02010.09020.081453.2213-14.230874.1768
16-0.0773-0.53040.12260-0.3832.95780.02310.11090.3141-0.0278-0.0034-0.06060.0237-0.001-0.0197-0.1590.00130.01180.0820.15320.057310.89437.29722.9342
171.2083-0.15180.21150.3613-0.35591.2425-0.0344-0.1060.17110.05760.0005-0.0212-0.1750.09580.0338-0.0437-0.0262-0.0226-0.0566-0.0236-0.063824.958923.473565.633
18-0.1054-0.2020.40490.24510.34230.24240.0037-0.0444-0.0034-0.0033-0.00710.0002-0.0581-0.01630.00340.1123-0.0184-0.0294-0.0268-0.08840.081139.2005-3.247840.5541
191.00690.01380.52520.72110.31943.8557-0.0417-0.16720.00150.0385-0.12750.0082-0.36820.52750.1691-0.1861-0.07-0.00830.05670.0978-0.214551.706515.948571.6358
20-0.56620.25082.18394.487-1.37671.1628-0.0061-0.0537-0.03550.0666-0.0432-0.20070.1481-0.02280.0493-0.047-0.0464-0.0568-0.11250.02390.115541.23831.390487.3499
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 37:58)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 59:256, 586:628)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 257:268)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 269:394, 425:585)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 395:424)
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 36:58)
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 59:256, 586:628)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 257:268)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 269:394, 425:585)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 395:424)
11X-RAY DIFFRACTION11CHAIN C AND (RESSEQ 40:58)
12X-RAY DIFFRACTION12CHAIN C AND (RESSEQ 59:256, 586:628)
13X-RAY DIFFRACTION13CHAIN C AND (RESSEQ 257:268)
14X-RAY DIFFRACTION14CHAIN C AND (RESSEQ 269:394, 425:585)
15X-RAY DIFFRACTION15CHAIN C AND (RESSEQ 395:424)
16X-RAY DIFFRACTION16CHAIN D AND (RESSEQ 35:58)
17X-RAY DIFFRACTION17CHAIN D AND (RESSEQ 59:256, 586:628)
18X-RAY DIFFRACTION18CHAIN D AND (RESSEQ 257:268)
19X-RAY DIFFRACTION19CHAIN D AND (RESSEQ 269:394, 425:585)
20X-RAY DIFFRACTION20CHAIN D AND (RESSEQ 395 :424)

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