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- PDB-5cfj: Structural and functional attributes of malaria parasite Ap4A hyd... -

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Basic information

Entry
Database: PDB / ID: 5cfj
TitleStructural and functional attributes of malaria parasite Ap4A hydrolase
ComponentsBIS(5'-nucleosyl)-tetraphosphatase (Diadenosine tetraphosphatase), putative
KeywordsHYDROLASE / AP4A / Purinergic signalling / Plasmodium / Nudix hydrolyse
Function / homology
Function and homology information


Detoxification of Reactive Oxygen Species / AMP biosynthetic process / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / ATP biosynthetic process / nucleotide binding
Similarity search - Function
Bis(5'-nucleosyl)-tetraphosphatase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.25 Å
AuthorsSharma, A. / Yogavel, M. / Sharma, A.
CitationJournal: Sci Rep / Year: 2016
Title: Structural and functional attributes of malaria parasite diadenosine tetraphosphate hydrolase
Authors: Sharma, A. / Yogavel, M. / Sharma, A.
History
DepositionJul 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Aug 16, 2017Group: Database references / Derived calculations / Category: pdbx_related_exp_data_set / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BIS(5'-nucleosyl)-tetraphosphatase (Diadenosine tetraphosphatase), putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1695
Polymers17,7751
Non-polymers3944
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-15 kcal/mol
Surface area7870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.491, 44.348, 94.677
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BIS(5'-nucleosyl)-tetraphosphatase (Diadenosine tetraphosphatase), putative / Ap4A hydrolase


Mass: 17775.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PFE1035c / Plasmid: pETM11 / Production host: Escherichia coli (E. coli)
References: UniProt: C0H4F3, bis(5'-nucleosyl)-tetraphosphatase (asymmetrical)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 1.94 Å3/Da / Density % sol: 36.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Lithium sulphate, sodium acetate, ethylene glycol, PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 47576 / % possible obs: 99.1 % / Redundancy: 5.3 % / Biso Wilson estimate: 14.92 Å2 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.019 / Rrim(I) all: 0.044 / Χ2: 0.943 / Net I/av σ(I): 36.228 / Net I/σ(I): 10 / Num. measured all: 251771
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.15-1.175.10.7323320.8650.3540.8140.88998.6
1.17-1.195.20.66522970.8190.3230.7420.90398.5
1.19-1.215.20.58323620.8870.2830.650.88498.3
1.21-1.245.20.57222730.8470.2770.6370.92197.4
1.24-1.275.10.45223420.9010.2190.5040.88798.2
1.27-1.35.20.40423220.9320.1950.450.91498.1
1.3-1.335.10.33923030.9410.1640.3780.9298
1.33-1.365.20.29423520.9540.1420.3270.92498.2
1.36-1.45.10.2423220.9710.1160.2670.9299.1
1.4-1.455.20.19823660.9780.0960.2210.93499.5
1.45-1.55.20.1524150.9860.0730.1670.915100
1.5-1.565.40.12123620.990.0580.1350.909100
1.56-1.635.50.10224000.990.0480.1130.972100
1.63-1.725.50.0923900.990.0420.0991.12100
1.72-1.835.60.08224040.9930.0380.0911.449100
1.83-1.975.60.06524250.9950.030.0711.568100
1.97-2.165.60.04124050.9980.0190.0451.012100
2.16-2.485.50.02624650.9990.0120.0290.633100
2.48-3.125.50.02124640.9990.010.0240.50299.8
3.12-505.10.0225750.9990.010.0230.62498

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Processing

Software
NameVersionClassification
HKL-2000data processing
Cootmodel building
PHENIX1.9_1692refinement
Coot3.15model building
RefinementMethod to determine structure: SAD / Resolution: 1.25→25.713 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1931 1865 4.98 %random selection
Rwork0.1701 35599 --
obs0.1712 37464 97.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.59 Å2 / Biso mean: 22.3357 Å2 / Biso min: 10.69 Å2
Refinement stepCycle: final / Resolution: 1.25→25.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1110 0 22 127 1259
Biso mean--36.11 31.43 -
Num. residues----140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061216
X-RAY DIFFRACTIONf_angle_d1.1441654
X-RAY DIFFRACTIONf_chiral_restr0.04176
X-RAY DIFFRACTIONf_plane_restr0.005212
X-RAY DIFFRACTIONf_dihedral_angle_d13.248458
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.25-1.28380.22381160.1662208232443
1.2838-1.32160.21131330.16462522265548
1.3216-1.36430.18331370.15132608274550
1.3643-1.4130.19551400.14412660280052
1.413-1.46960.21091440.13852722286652
1.4696-1.53650.15271420.13132703284552
1.5365-1.61750.1821420.13472699284152
1.6175-1.71880.15931440.13922746289053
1.7188-1.85140.17981450.14492756290153
1.8514-2.03770.17491430.14452717286053
2.0377-2.33240.16291500.15132853300355
2.3324-2.93790.19391590.1963169332861
2.9379-25.71840.21951700.19283236340662

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