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- PDB-8aih: Crystal Structure of Enterococcus faecium Nicotinate Nucleotide A... -

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Basic information

Entry
Database: PDB / ID: 8aih
TitleCrystal Structure of Enterococcus faecium Nicotinate Nucleotide Adenylyltransferase at 1.9 Angstroms Resolution
ComponentsProbable nicotinate-nucleotide adenylyltransferase
KeywordsTRANSFERASE / Enterococcus faecium / Nicotinate nucleotide adenylyltransferase / ATP / Adenine
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
DIHYDROGENPHOSPHATE ION / Probable nicotinate-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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: Int.J.Biol.Macromol. / Year: 2023
Title: Obtaining high yield recombinant Enterococcus faecium nicotinate nucleotide adenylyltransferase for X-ray crystallography and biophysical studies.
Authors: Jeje, O. / Pandian, R. / Sayed, Y. / Achilonu, I.
History
DepositionJul 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9213
Polymers24,7281
Non-polymers1932
Water1,892105
1
A: Probable nicotinate-nucleotide adenylyltransferase
hetero molecules

A: Probable nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8436
Polymers49,4562
Non-polymers3864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y,-z+1/21
Buried area2740 Å2
ΔGint-37 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.650, 64.540, 108.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121

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Components

#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.: 1
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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-2HP / DIHYDROGENPHOSPHATE ION


Mass: 96.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O4P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.16 Å3/Da / Density % sol: 43.1 % / Description: Bipyramid
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 15 mg/mL EfNNAT in 50 mM HEPES, 150 mM NaCl, 2mM DTT, 0.02% NaN3 at pH 7.2 with the crystallization condition of 0.1 M Tris (pH 8.5), 2.0 M Ammonium sulfate

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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
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→45.32 Å / Num. obs: 17988 / % possible obs: 99.9 % / Redundancy: 12.8 % / Biso Wilson estimate: 33.03 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.217 / Rpim(I) all: 0.063 / Rrim(I) all: 0.226 / Net I/σ(I): 5.9
Reflection shellResolution: 1.9→1.93 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 874 / CC1/2: 0.283 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology structure generated by AlphaFold

Resolution: 1.9→45.32 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 36.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2787 921 5.12 %
Rwork0.236 17050 -
obs0.2384 17971 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 170.5 Å2 / Biso mean: 54.5859 Å2 / Biso min: 21.8 Å2
Refinement stepCycle: final / Resolution: 1.9→45.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1494 0 10 105 1609
Biso mean--70.45 59.02 -
Num. residues----184
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-20.37631240.33032373249799
2-2.130.32821220.314924102532100
2.13-2.290.3531100.303324392549100
2.29-2.520.34641440.290424142558100
2.52-2.880.33351190.275124242543100
2.89-3.630.30581600.241824222582100
3.63-45.320.22751420.192625682710100
Refinement TLS params.Method: refined / Origin x: -6.4901 Å / Origin y: -1.1206 Å / Origin z: 11.2882 Å
111213212223313233
T0.2704 Å20.0541 Å2-0.0682 Å2-0.2524 Å2-0.0595 Å2--0.2708 Å2
L0.9615 °20.8592 °2-0.6906 °2-3.707 °2-1.4037 °2--4.3191 °2
S0.0575 Å °0.0919 Å °-0.1044 Å °-0.0663 Å °0.0466 Å °-0.1111 Å °0.3626 Å °0.0732 Å °-0.0803 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA23 - 212
2X-RAY DIFFRACTION1allA302 - 303
3X-RAY DIFFRACTION1allW1 - 105

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