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- PDB-5lm3: Plasmodium falciparum nicotinic acid mononucleotide adenylyltrans... -

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Basic information

Entry
Database: PDB / ID: 5lm3
TitlePlasmodium falciparum nicotinic acid mononucleotide adenylyltransferase complexed with APC
ComponentsNicotinate-nucleotide adenylyltransferase
KeywordsTRANSFERASE / Nicotinic acid mononucleotide adenylyltransferase / NaMNAT / protein crystallography / Plasmodium falciparum / drug target / malaria / NAD metabolism
Function / homology
Function and homology information


nicotinamide-nucleotide adenylyltransferase / nicotinate-nucleotide adenylyltransferase activity / NAD biosynthetic process / cytoplasm
Similarity search - Function
Nicotinate/nicotinamide nucleotide adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / nicotinamide-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBathke, J. / Fritz-Wolf, K. / Rahlfs, S. / Brandstaether, C. / Burkhardt, A. / Becker, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationBE1540/23-1 within SPP 1710 Germany
CitationJournal: J. Mol. Biol. / Year: 2016
Title: Structural and Functional Characterization of Plasmodium falciparum Nicotinic Acid Mononucleotide Adenylyltransferase.
Authors: Bathke, J. / Fritz-Wolf, K. / Brandstadter, C. / Burkhardt, A. / Jortzik, E. / Rahlfs, S. / Becker, K.
History
DepositionJul 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Feb 8, 2017Group: Data collection
Revision 1.3Mar 29, 2017Group: Database references
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0133
Polymers25,4451
Non-polymers5672
Water59433
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint8 kcal/mol
Surface area10490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.240, 38.920, 62.710
Angle α, β, γ (deg.)90.00, 113.54, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nicotinate-nucleotide adenylyltransferase /


Mass: 25445.338 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: PF3D7_1327600 / Production host: Escherichia coli (E. coli) / Strain (production host): KRX
References: UniProt: Q8IE38, nicotinate-nucleotide adenylyltransferase
#2: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 14 mg/ml, 0.15 M bicine, pH 8.5 and 19% PEG 6000, 5mM APC

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033208 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033208 Å / Relative weight: 1
ReflectionResolution: 2.5→32.2 Å / Num. obs: 8537 / % possible obs: 98.2 % / Redundancy: 3.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.123 / Rsym value: 0.104 / Net I/σ(I): 8.16
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.815 / Mean I/σ(I) obs: 2.05 / CC1/2: 0.831 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDS20151231data reduction
PHENIX1.10.1_2155phasing
Coot0.8.3model building
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LLT

5llt


Resolution: 2.5→32.23 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.263 516 6.05 %
Rwork0.2114 --
obs0.2145 8522 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→32.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1688 0 35 33 1756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011769
X-RAY DIFFRACTIONf_angle_d0.3882394
X-RAY DIFFRACTIONf_dihedral_angle_d10.3551043
X-RAY DIFFRACTIONf_chiral_restr0.042261
X-RAY DIFFRACTIONf_plane_restr0.004289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4998-2.75130.42831270.34191959X-RAY DIFFRACTION98
2.7513-3.14910.32641290.24451989X-RAY DIFFRACTION99
3.1491-3.96640.25341310.1992001X-RAY DIFFRACTION98
3.9664-32.23220.21191290.17922057X-RAY DIFFRACTION98

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