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- PDB-1kku: Crystal structure of nuclear human nicotinamide mononucleotide ad... -

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Basic information

Entry
Database: PDB / ID: 1kku
TitleCrystal structure of nuclear human nicotinamide mononucleotide adenylyltransferase
ComponentsNICOTINAMIDE MONONUCLEOTIDE ADENYLYLTRANSFERASE
KeywordsTRANSFERASE / alpha/beta structure - Rossmann fold
Function / homology
Function and homology information


negative regulation of apoptotic DNA fragmentation / protein ADP-ribosyltransferase-substrate adaptor activity / nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / nucleotide biosynthetic process / nicotinate-nucleotide adenylyltransferase activity / Nicotinate metabolism / ATP generation from poly-ADP-D-ribose / NAD+ biosynthetic process ...negative regulation of apoptotic DNA fragmentation / protein ADP-ribosyltransferase-substrate adaptor activity / nicotinamide-nucleotide adenylyltransferase / nicotinamide-nucleotide adenylyltransferase activity / nicotinate-nucleotide adenylyltransferase / nucleotide biosynthetic process / nicotinate-nucleotide adenylyltransferase activity / Nicotinate metabolism / ATP generation from poly-ADP-D-ribose / NAD+ biosynthetic process / neuron projection maintenance / response to wounding / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / nuclear body / negative regulation of DNA-templated transcription / chromatin / nucleoplasm / ATP binding / identical protein binding / nucleus
Similarity search - Function
Nicotinamide/nicotinate mononucleotide adenylyltransferase, eukaryotic / : / 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
Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsGaravaglia, S. / D'Angelo, I. / Emanuelli, M. / Carnevali, F. / Pierella, F. / Magni, G. / Rizzi, M.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structure of human NMN adenylyltransferase. A key nuclear enzyme for NAD homeostasis.
Authors: Garavaglia, S. / D'Angelo, I. / Emanuelli, M. / Carnevali, F. / Pierella, F. / Magni, G. / Rizzi, M.
History
DepositionDec 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NICOTINAMIDE MONONUCLEOTIDE ADENYLYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)32,0171
Polymers32,0171
Non-polymers00
Water1,00956
1
A: NICOTINAMIDE MONONUCLEOTIDE ADENYLYLTRANSFERASE
x 6


Theoretical massNumber of molelcules
Total (without water)192,0996
Polymers192,0996
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
crystal symmetry operation11_555-x+y,y,-z+1/21
Unit cell
Length a, b, c (Å)147.459, 147.459, 61.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein NICOTINAMIDE MONONUCLEOTIDE ADENYLYLTRANSFERASE / NMN adenylyltransferase


Mass: 32016.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9HAN9, nicotinamide-nucleotide adenylyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: ammonium sulfate, Tris, isopropanol, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.02 MTris1droppH8.0
22 mMATP1drop
32 mM1dropMgCl2
420 mg/mlprotein1drop
51.8 Mammonium sulfate1reservoir
60.1 MTris1reservoirpH8.1
74 %(v/v)isopropyl alcohol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 2, 2000
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 14091 / Num. obs: 14091 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.075
Reflection shellResolution: 2.5→2.6 Å / % possible all: 99
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 14056 / Rmerge(I) obs: 0.075

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Processing

Software
NameVersionClassification
SHELXSphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.5→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.284 965 RANDOM
Rwork0.236 --
all0.25 14091 -
obs0.247 14091 -
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 0 56 1806
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_deg2
Refinement
*PLUS
Rfactor all: 0.25 / Rfactor obs: 0.234 / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_planar_d / Dev ideal: 0.011

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