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- PDB-8aii: High Resolution Crystal Structure of Enterococcus faecium Nicotin... -

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Basic information

Entry
Database: PDB / ID: 8aii
TitleHigh Resolution Crystal Structure of Enterococcus faecium Nicotinate Nucleotide Adenylyltransferase Complexed with Adenine
ComponentsProbable nicotinate-nucleotide adenylyltransferase
KeywordsTRANSFERASE / Enterococcus / faecium / Nicotinate / nucleotide / adenylyltransferase / 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
ADENINE / Probable nicotinate-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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)24,9844
Polymers24,7281
Non-polymers2553
Water1,62190
1
A: Probable nicotinate-nucleotide adenylyltransferase
hetero molecules

A: Probable nicotinate-nucleotide adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9678
Polymers49,4562
Non-polymers5116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455-x-1/2,y,-z1
Buried area3100 Å2
ΔGint-48 kcal/mol
Surface area17170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.511, 65.644, 108.373
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-432-

HOH

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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-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.15 Å3/Da / Density % sol: 42.95 % / Description: Bipyramid
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 15 mg/mL EfNNAT in 50mM HEPES, 2mM DTT, 150mM NaCl, 0.02% NaN3 at pH 7.2 with the crystallization buffer consisting of 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS (pH 5.5), 25% w/v Polyethylene glycol 3350

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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: 1.82→45.269 Å / Num. obs: 19984 / % possible obs: 98.7 % / Redundancy: 13.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.033 / Rrim(I) all: 0.121 / Net I/σ(I): 10.4
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 14 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 979 / CC1/2: 0.418 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
DIALSdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology structure generated by AlphaFold

Resolution: 1.82→45.269 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2332 935 4.84 %
Rwork0.2057 18392 -
obs0.2071 19327 94.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.33 Å2 / Biso mean: 56.9304 Å2 / Biso min: 23.48 Å2
Refinement stepCycle: final / Resolution: 1.82→45.269 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1468 0 16 90 1574
Biso mean--69.9 61.19 -
Num. residues----181
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8201-1.9160.4369890.3922193271
1.916-2.03610.28081280.311266998
2.0361-2.19330.28881540.2571267898
2.1933-2.4140.25441400.2132270899
2.414-2.76330.25241310.2144274899
2.7633-3.48120.23951450.2084276599
3.4812-45.2690.20251480.1757289299
Refinement TLS params.Method: refined / Origin x: -14.6535 Å / Origin y: 9.8057 Å / Origin z: -15.7478 Å
111213212223313233
T0.3088 Å2-0.0554 Å20.0615 Å2-0.3345 Å2-0.0616 Å2--0.2701 Å2
L3.2216 °2-0.4614 °21.0081 °2-1.8928 °20.4186 °2--4.7552 °2
S0.1069 Å °0.1412 Å °0.1797 Å °-0.1551 Å °0.1284 Å °-0.3287 Å °-0.2677 Å °0.631 Å °-0.1677 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA24 - 212
2X-RAY DIFFRACTION1allA292 - 301
3X-RAY DIFFRACTION1allB1 - 91

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