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- PDB-6rmd: Structure of ATP bound Plasmodium falciparum IMP-nucleotidase -

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Basic information

Entry
Database: PDB / ID: 6rmd
TitleStructure of ATP bound Plasmodium falciparum IMP-nucleotidase
Components(IMP-specific 5'-nucleotidase, putative) x 2
KeywordsHYDROLASE / nucleotidase / activator / complex / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


nicotinamide riboside biosynthetic process / nicotinic acid riboside biosynthetic process / inosine salvage / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity / IMP catabolic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
IMP-specific 5-nucleotidase / IMP-specific 5'-nucleotidase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / IMP-specific 5'-nucleotidase 1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsCarrique, L. / Ballut, L. / Violot, S. / Aghajari, N.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-17-CE11-0032 France
CitationJournal: Nat Commun / Year: 2020
Title: Structure and catalytic regulation of Plasmodium falciparum IMP specific nucleotidase.
Authors: Carrique, L. / Ballut, L. / Shukla, A. / Varma, N. / Ravi, R. / Violot, S. / Srinivasan, B. / Ganeshappa, U.T. / Kulkarni, S. / Balaram, H. / Aghajari, N.
History
DepositionMay 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 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: IMP-specific 5'-nucleotidase, putative
D: IMP-specific 5'-nucleotidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9896
Polymers94,2952
Non-polymers6934
Water1629
1
A: IMP-specific 5'-nucleotidase, putative
D: IMP-specific 5'-nucleotidase, putative
hetero molecules

A: IMP-specific 5'-nucleotidase, putative
D: IMP-specific 5'-nucleotidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,97812
Polymers188,5914
Non-polymers1,3878
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area14790 Å2
ΔGint-46 kcal/mol
Surface area62000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.690, 210.690, 106.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein IMP-specific 5'-nucleotidase, putative


Mass: 50895.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Gene: PF3D7_1206100 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A144A134, 5'-nucleotidase
#2: Protein IMP-specific 5'-nucleotidase, putative


Mass: 43400.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Gene: PF3D7_1206100 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A144A134, 5'-nucleotidase
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.27 Å3/Da / Density % sol: 62.43 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium malonate pH 5.0, 12% (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 2.5→47.43 Å / Num. obs: 48313 / % possible obs: 99.9 % / Redundancy: 12.6 % / CC1/2: 1 / Net I/σ(I): 18.4
Reflection shellResolution: 2.5→2.61 Å / Num. unique obs: 5874 / CC1/2: 0.4

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→47.4 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.1
RfactorNum. reflection% reflection
Rfree0.2454 1730 5 %
Rwork0.2002 --
obs0.2025 34611 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6263 0 43 9 6315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056452
X-RAY DIFFRACTIONf_angle_d0.7248759
X-RAY DIFFRACTIONf_dihedral_angle_d11.53874
X-RAY DIFFRACTIONf_chiral_restr0.046990
X-RAY DIFFRACTIONf_plane_restr0.0031115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.880.3831410.32222681X-RAY DIFFRACTION100
2.88-2.980.34371410.28472674X-RAY DIFFRACTION100
2.98-3.080.32721420.26272701X-RAY DIFFRACTION100
3.08-3.210.32171420.2532711X-RAY DIFFRACTION100
3.21-3.350.33061420.25482695X-RAY DIFFRACTION100
3.35-3.530.22161430.21012716X-RAY DIFFRACTION100
3.53-3.750.25941430.1882712X-RAY DIFFRACTION100
3.75-4.040.24251430.18442720X-RAY DIFFRACTION100
4.04-4.440.20651450.15822752X-RAY DIFFRACTION100
4.44-5.090.1851450.15232764X-RAY DIFFRACTION100
5.09-6.40.26371480.21782798X-RAY DIFFRACTION100
6.41-47.430.23321550.20072957X-RAY DIFFRACTION100
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)
11.65730.8909-0.13171.39480.63531.3043-0.06650.24330.5693-0.0836-0.0947-0.10650.2364-0.06440.13231.12820.046-0.01781.12360.0021.068874.0963-30.0956-0.8757
20.5751-0.3677-0.15455.1443-0.82142.04150.00550.01030.1405-0.4276-0.22480.18950.16610.07580.19610.42690.017-0.04790.56750.09080.479366.1531-36.4197-15.597
31.07050.07460.56282.62730.03193.8690.01770.13660.25-0.3775-0.10480.3146-0.01820.06810.07750.51570.03340.00170.36010.1320.709265.1311-10.6668-6.497
41.99670.17240.44513.1828-0.73612.5859-0.04560.17520.1802-0.5713-0.19350.17590.02310.32490.19580.76930.0628-0.06010.61960.11240.696466.5347-30.0127-19.0682
52.5501-0.6030.14482.5113-0.57962.33370.44750.2458-0.0156-0.6333-0.4776-0.18911.23280.94540.04150.95070.33850.18110.8450.18770.513471.2484-62.8826-1.2948
64.3873-1.41111.34092.9439-1.25493.12060.8183-0.2928-0.8036-0.4276-0.2598-0.11480.7896-0.2159-0.53440.85940.0592-0.14580.55350.15870.698875.7719-82.00822.755
70.42750.18380.75513.49480.59331.3580.3627-0.1224-0.1861-0.0903-0.2608-0.49340.1295-0.0575-0.1280.58630.14980.01670.79730.34310.845286.4389-65.31131.3717
85.1816-1.0867-1.74474.18260.19454.46660.5403-0.452-0.0574-0.3869-0.67780.2485-0.20380.25260.11960.84360.21510.00710.74370.13230.464373.0935-72.31914.0761
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 60 )
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 211 )
3X-RAY DIFFRACTION3chain 'A' and (resid 212 through 382 )
4X-RAY DIFFRACTION4chain 'A' and (resid 383 through 444 )
5X-RAY DIFFRACTION5chain 'D' and (resid 59 through 144 )
6X-RAY DIFFRACTION6chain 'D' and (resid 145 through 265 )
7X-RAY DIFFRACTION7chain 'D' and (resid 266 through 397 )
8X-RAY DIFFRACTION8chain 'D' and (resid 398 through 430 )

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