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

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Basic information

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


nicotinate-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
NICOTINIC ACID ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Nicotinamide/nicotinic acid mononucleotide adenylyltransferase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBathke, J. / Fritz-Wolf, K. / Brandstaedter, C. / Rahlfs, S. / Becker, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation(BE1540/23-1 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 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Mar 29, 2017Group: Database references
Revision 1.3Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
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
B: Nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,99215
Polymers50,8912
Non-polymers2,10213
Water2,774154
1
A: Nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5278
Polymers25,4451
Non-polymers1,0827
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4657
Polymers25,4451
Non-polymers1,0206
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.970, 52.110, 61.250
Angle α, β, γ (deg.)93.94, 90.00, 109.85
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Nicotinate-nucleotide adenylyltransferase


Mass: 25445.338 Da / Num. of mol.: 2
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 KRX (bacteria)
References: UniProt: Q8IE38, nicotinate-nucleotide adenylyltransferase
#2: Chemical ChemComp-DND / NICOTINIC ACID ADENINE DINUCLEOTIDE / DEAMIDO-NAD+


Mass: 665.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N6O15P2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: 16 mg/ml, 0.1 M bicine, pH 8.2 and 18% PEG 6000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 19100 / % possible obs: 83.3 % / Redundancy: 1.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rsym value: 0.034 / Net I/av σ(I): 14.17 / Net I/σ(I): 14.1
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 1.65 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 4.97 / CC1/2: 0.969 / % possible all: 41.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
CNSphasing
Cootmodel building
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H29

2h29


Resolution: 2.2→39.603 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 27.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2345 1144 5.99 %
Rwork0.1685 --
obs0.1724 19086 83.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→39.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 138 154 3740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073675
X-RAY DIFFRACTIONf_angle_d0.9764954
X-RAY DIFFRACTIONf_dihedral_angle_d14.8561333
X-RAY DIFFRACTIONf_chiral_restr0.053538
X-RAY DIFFRACTIONf_plane_restr0.006598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2002-2.30030.3437760.23261188X-RAY DIFFRACTION44
2.3003-2.42160.31131070.19551692X-RAY DIFFRACTION63
2.4216-2.57330.30221530.18722411X-RAY DIFFRACTION90
2.5733-2.77190.22171610.17312519X-RAY DIFFRACTION93
2.7719-3.05080.26661600.17612520X-RAY DIFFRACTION94
3.0508-3.4920.25581610.16692521X-RAY DIFFRACTION93
3.492-4.39860.19231620.14862532X-RAY DIFFRACTION94
4.3986-39.60980.21391640.16642559X-RAY DIFFRACTION95

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