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- PDB-9fyb: Structural Insights into the NMN Complex of Nicotinate Nucleotide... -

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Basic information

Entry
Database: PDB / ID: 9fyb
TitleStructural Insights into the NMN Complex of Nicotinate Nucleotide Adenylyltransferase from Enterococcus faecium via Co-Crystallization Studies
ComponentsProbable nicotinate-nucleotide adenylyltransferase
KeywordsTRANSFERASE / Enterococcus faecium / Nicotinate / nucleotide / adenylyltransferase / NMN / EfNaMNAT / EfNNAT
Function / homology
Function and homology information


nicotinate-nucleotide adenylyltransferase / nicotinate-nucleotide adenylyltransferase activity / NAD biosynthetic process / ATP binding
Similarity search - Function
Nicotinate/nicotinamide nucleotide adenylyltransferase / Cytidylyltransferase-like / Cytidyltransferase-like domain / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / Probable nicotinate-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsPandian, R. / Jeje, O.A. / Sayed, Y. / Achilonu, I.A.
Funding support United Kingdom, South Africa, 2items
OrganizationGrant numberCountry
Science and Technology Funding CouncilST/R002754/1 United Kingdom
South African Medical Research Council self-initiated research grant (SAMRC SIR Grant)ACHL019 South Africa
CitationJournal: To be published
Title: Structural Insights into the NMN Complex of Nicotinate Nucleotide Adenylyltransferase from Enterococcus faecium via Co-Crystallization Studies
Authors: Jeje, O.A. / Pandian, R. / Sayed, Y. / Achilonu, I.A.
History
DepositionJul 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable nicotinate-nucleotide adenylyltransferase
B: Probable nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,74813
Polymers49,4562
Non-polymers1,29211
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-18 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.449, 107.344, 62.344
Angle α, β, γ (deg.)90.00, 128.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-304-

PEG

21A-310-

MG

31B-417-

HOH

41B-493-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Probable nicotinate-nucleotide adenylyltransferase / Deamido-NAD(+) diphosphorylase / Deamido-NAD(+) pyrophosphorylase / Nicotinate mononucleotide ...Deamido-NAD(+) diphosphorylase / Deamido-NAD(+) pyrophosphorylase / Nicotinate mononucleotide adenylyltransferase / NaMN adenylyltransferase


Mass: 24728.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria)
Gene: nadD, nadD_1, B1P95_04405, BU194_05695, DTPHA_1401727, HMPREF3199_01612
Production host: Escherichia coli (E. coli)
References: UniProt: A0A133MWI0, nicotinate-nucleotide adenylyltransferase

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Non-polymers , 6 types, 230 molecules

#2: Chemical ChemComp-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE


Mass: 335.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.55 Å3/Da / Density % sol: 51.8 % / Description: Needle/block
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 15 mg/mL EfNNAT in 50 mM HEPES (pH 7.2), 150 mM NaCl, 0.02 % (w/v) NaN3 and 1 mM DTT, 2 mM NMN and 5mM MgCl2 with the crystallization condition consisting of 1.26 M sodium phosphate ...Details: 15 mg/mL EfNNAT in 50 mM HEPES (pH 7.2), 150 mM NaCl, 0.02 % (w/v) NaN3 and 1 mM DTT, 2 mM NMN and 5mM MgCl2 with the crystallization condition consisting of 1.26 M sodium phosphate monobasic monohydrate, 0.14M potassium phosphate dibasic (pH 5.6) and 20% 3350 polyethylene glycol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.84→48.45 Å / Num. obs: 41063 / % possible obs: 98.28 % / Redundancy: 7.1 % / Biso Wilson estimate: 43.47 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.04 / Rrim(I) all: 0.106 / Net I/σ(I): 11.4
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 0.3 / Num. unique obs: 2032 / CC1/2: 0.226 / % possible all: 97.55

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata reduction
DIALSdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→46.59 Å / SU ML: 0.42 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 36.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.268 2005 4.95 %
Rwork0.209 --
obs0.212 40488 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.84→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2982 0 71 219 3272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093120
X-RAY DIFFRACTIONf_angle_d1.0664229
X-RAY DIFFRACTIONf_dihedral_angle_d11.303422
X-RAY DIFFRACTIONf_chiral_restr0.065460
X-RAY DIFFRACTIONf_plane_restr0.009532
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.890.5191170.46122344X-RAY DIFFRACTION82
1.89-1.940.47961380.42982666X-RAY DIFFRACTION95
1.94-1.990.38721470.37662713X-RAY DIFFRACTION97
1.99-2.060.35731440.32912754X-RAY DIFFRACTION97
2.06-2.130.32851310.28472781X-RAY DIFFRACTION97
2.13-2.220.30661490.25282765X-RAY DIFFRACTION98
2.22-2.320.28061270.2342768X-RAY DIFFRACTION98
2.32-2.440.28521460.2182784X-RAY DIFFRACTION98
2.44-2.590.26091350.21192808X-RAY DIFFRACTION99
2.59-2.790.29011670.2032788X-RAY DIFFRACTION99
2.79-3.080.2781250.20492813X-RAY DIFFRACTION99
3.08-3.520.22561490.18982822X-RAY DIFFRACTION99
3.52-4.430.23391570.16422838X-RAY DIFFRACTION99
4.44-46.590.26491730.20452839X-RAY DIFFRACTION99

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