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- PDB-1kaq: Structure of Bacillus subtilis Nicotinic Acid Mononucleotide Aden... -

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Basic information

Entry
Database: PDB / ID: 1kaq
TitleStructure of Bacillus subtilis Nicotinic Acid Mononucleotide Adenylyl Transferase
ComponentsNICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE
KeywordsTRANSFERASE / Rossmann fold / NaAD
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 / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINIC ACID ADENINE DINUCLEOTIDE / Nicotinate-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Combined MAD, molecular replacement phases / Resolution: 3.2 Å
AuthorsOlland, A.M. / Underwood, K.W. / Czerwinski, R.M. / Lo, M.C. / Aulabaugh, A. / Bard, J. / Stahl, M.L. / Somers, W.S. / Sullivan, F.X. / Chopra, R.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Identification, characterization, and crystal structure of Bacillus subtilis nicotinic acid mononucleotide adenylyltransferase.
Authors: Olland, A.M. / Underwood, K.W. / Czerwinski, R.M. / Lo, M.C. / Aulabaugh, A. / Bard, J. / Stahl, M.L. / Somers, W.S. / Sullivan, F.X. / Chopra, R.
History
DepositionNov 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Nov 19, 2014Group: Derived calculations
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE
B: NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE
C: NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE
D: NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE
E: NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE
F: NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,70612
Polymers135,7136
Non-polymers3,9936
Water00
1
A: NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE
D: NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5694
Polymers45,2382
Non-polymers1,3312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-16 kcal/mol
Surface area16850 Å2
MethodPISA
2
B: NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE
C: NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5694
Polymers45,2382
Non-polymers1,3312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-19 kcal/mol
Surface area16820 Å2
MethodPISA
3
E: NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE
F: NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5694
Polymers45,2382
Non-polymers1,3312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-19 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.310, 108.784, 177.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein
NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE / E.C.2.7.7.18 / DEAMIDO-NAD(+) PYROPHOSPHORYLASE / DEAMIDO-NAD(+) DIPHOSPHORYLASE / NICOTINATE MONONUCLEOTIDE ...DEAMIDO-NAD(+) PYROPHOSPHORYLASE / DEAMIDO-NAD(+) DIPHOSPHORYLASE / NICOTINATE MONONUCLEOTIDE ADENYLYLTRANSFERASE / NAMN ADENYLYLTRANSFERASE / YqeJ


Mass: 22618.902 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: nadD / Plasmid: pML208 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P54455, nicotinate-nucleotide adenylyltransferase
#2: Chemical
ChemComp-DND / NICOTINIC ACID ADENINE DINUCLEOTIDE / DEAMIDO-NAD+


Mass: 665.418 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N6O15P2

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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: 2.78 Å3/Da / Density % sol: 55.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, Magnesium Acetate, xylitol, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 291K
Crystal grow
*PLUS
Temperature: 18 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
114 mg/mlprotein1drop
22 mMNaAD1drop
350 mMHEPES1droppH7.5
450 mM1dropNaCl
520 %PEG33501reservoir
6100 mMmagnesium acetate1reservoir
730 %(w/v)xylitol1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9791, 0.9639
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2001
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.96391
ReflectionResolution: 3.2→15 Å / Num. all: 25491 / Num. obs: 24599 / % possible obs: 96.5 % / Observed criterion σ(I): 2
Reflection shellResolution: 3.2→3.31 Å / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 5.6 / Num. unique all: 1920 / % possible all: 84
Reflection
*PLUS
Highest resolution: 3.2 Å / Num. measured all: 80499 / Rmerge(I) obs: 0.147
Reflection shell
*PLUS
% possible obs: 84 % / Rmerge(I) obs: 0.289

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: Combined MAD, molecular replacement phases
Resolution: 3.2→15 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1157 4.8 %random
Rwork0.279 ---
obs-23942 --
Refinement stepCycle: LAST / Resolution: 3.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9004 0 264 0 9268
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.913
LS refinement shellResolution: 3.2→3.23 Å
RfactorNum. reflection
Rfree0.3379 32
Rwork0.3957 -
obs-618
Refinement
*PLUS
Highest resolution: 3.2 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.2975 / Rfactor Rwork: 0.2564
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.3379 / Rfactor Rwork: 0.3957

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