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

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Basic information

Entry
Database: PDB / ID: 1kam
TitleStructure of Bacillus subtilis Nicotinic Acid Mononucleotide Adenylyl Transferase
ComponentsNICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE
KeywordsTRANSFERASE / Rossmann fold
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
Nicotinate-nucleotide adenylyltransferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 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 1.4Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE
D: NICOTINATE-NUCLEOTIDE ADENYLYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)90,4764
Polymers90,4764
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11290 Å2
ΔGint-67 kcal/mol
Surface area29950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.977, 126.103, 70.579
Angle α, β, γ (deg.)90.00, 92.73, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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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.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG3350, Magnesium chloride, 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
250 mMHEPES1droppH7.5
350 mM1dropNaCl
48 %PEG33501reservoir
5100 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9792, 0.9567
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2001
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.95671
ReflectionResolution: 2→20 Å / Num. all: 51680 / Num. obs: 51628 / % possible obs: 99.9 % / Observed criterion σ(I): 2
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.4 / Num. unique all: 5108 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. obs: 51680 / Num. measured all: 196259 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.47

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2163 5 %random
Rwork0.222 ---
all-44673 --
obs-43266 96.9 %-
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5848 0 0 139 5987
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.347
LS refinement shellResolution: 2.1→2.12 Å
RfactorNum. reflection
Rfree0.4063 41
Rwork0.2764 -
obs-935
Refinement
*PLUS
Highest resolution: 2.1 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.2544 / Rfactor Rwork: 0.2221
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.4063 / Rfactor Rwork: 0.2764

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