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

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Basic information

Entry
Database: PDB / ID: 5cfi
TitleStructural and functional attributes of malaria parasite Ap4A hydrolase
ComponentsBIS(5'-nucleosyl)-tetraphosphatase (Diadenosine tetraphosphatase), putative
KeywordsHYDROLASE / Ap4A / Nudix hydrolyse / Plasmodium / Purinergic
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 / : / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...Bis(5'-nucleosyl)-tetraphosphatase / : / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical]
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 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

Downloads & links

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Assembly

Deposited unit
A: BIS(5'-nucleosyl)-tetraphosphatase (Diadenosine tetraphosphatase), putative
B: BIS(5'-nucleosyl)-tetraphosphatase (Diadenosine tetraphosphatase), putative
C: BIS(5'-nucleosyl)-tetraphosphatase (Diadenosine tetraphosphatase), putative
D: BIS(5'-nucleosyl)-tetraphosphatase (Diadenosine tetraphosphatase), putative


Theoretical massNumber of molelcules
Total (without water)71,1014
Polymers71,1014
Non-polymers00
Water1,13563
1
B: BIS(5'-nucleosyl)-tetraphosphatase (Diadenosine tetraphosphatase), putative


Theoretical massNumber of molelcules
Total (without water)17,7751
Polymers17,7751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: BIS(5'-nucleosyl)-tetraphosphatase (Diadenosine tetraphosphatase), putative


Theoretical massNumber of molelcules
Total (without water)17,7751
Polymers17,7751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BIS(5'-nucleosyl)-tetraphosphatase (Diadenosine tetraphosphatase), putative


Theoretical massNumber of molelcules
Total (without water)17,7751
Polymers17,7751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: BIS(5'-nucleosyl)-tetraphosphatase (Diadenosine tetraphosphatase), putative


Theoretical massNumber of molelcules
Total (without water)17,7751
Polymers17,7751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)163.310, 64.245, 61.405
Angle α, β, γ (deg.)90.000, 100.080, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 17775.174 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PFE1035c / Plasmid: pETM11 / Details (production host): Expression vector / Production host: Escherichia coli (E. coli)
References: UniProt: C0H4F3, bis(5'-nucleosyl)-tetraphosphatase (asymmetrical)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: peg, potassium nitrate, sodium bromide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97625 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 19340 / % possible obs: 98.3 % / Redundancy: 5 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.048 / Rrim(I) all: 0.109 / Χ2: 0.977 / Net I/av σ(I): 18.585 / Net I/σ(I): 6.1 / Num. measured all: 96922
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6450.6189530.8350.2960.6870.60497.9
2.64-2.6950.569680.8310.270.6240.59398.2
2.69-2.745.20.4269600.9240.2030.4730.61799.2
2.74-2.850.419630.9230.1960.4550.66798.7
2.8-2.865.20.329570.9560.1520.3550.65999.5
2.86-2.935.10.2779770.9660.1320.3080.68898.2
2.93-35.10.249610.9790.1150.2660.73899.7
3-3.085.10.29770.9770.0950.2210.80498.5
3.08-3.175.30.1779610.9840.0840.1970.8199.4
3.17-3.285.20.1429710.9890.0680.1570.86198.8
3.28-3.395.10.1219750.9920.0580.1350.95298.7
3.39-3.535.10.0999530.9920.0480.111.00198.9
3.53-3.6950.099820.9920.0440.11.00598.9
3.69-3.884.90.0879570.9940.0440.0981.11298
3.88-4.124.90.0729710.9970.0360.081.05798.2
4.12-4.444.80.0629470.9960.0310.071.07195.9
4.44-4.894.60.0629360.9940.0320.071.31795
4.89-5.594.80.0659690.9930.0330.0741.45696.8
5.59-7.0350.0689850.9940.0340.0761.34199.2
7.03-304.90.06610170.9950.0350.0752.27498.5

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Processing

Software
NameVersionClassification
HKL-2000data processing
DNAdata collection
HKL-20003.15data scaling
PHASERphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: SAD / Resolution: 2.6→25.094 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 32.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2743 1913 10.01 %
Rwork0.2104 17202 -
obs0.2169 19115 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.49 Å2 / Biso mean: 54.6975 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.6→25.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 0 63 4258
Biso mean---49.03 -
Num. residues----549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094317
X-RAY DIFFRACTIONf_angle_d1.1565847
X-RAY DIFFRACTIONf_chiral_restr0.045627
X-RAY DIFFRACTIONf_plane_restr0.005762
X-RAY DIFFRACTIONf_dihedral_angle_d13.6651516
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.66490.39251380.28961243138198
2.6649-2.73690.32021340.26211203133799
2.7369-2.81740.33781370.24351233137099
2.8174-2.90820.36611360.24141224136099
2.9082-3.01190.32181360.25841222135899
3.0119-3.13230.31351350.23091206134199
3.1323-3.27460.3491370.22681233137099
3.2746-3.44680.25271360.20191229136598
3.4468-3.66220.28661380.20111245138399
3.6622-3.94390.29231370.20161226136398
3.9439-4.3390.22841350.17071224135997
4.339-4.96260.24291320.16661183131594
4.9626-6.23650.25211370.21431237137498
6.2365-25.09520.23171450.224112941439100

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