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- PDB-2qg6: Crystal structure of human nicotinamide riboside kinase (NRK1) in... -

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Basic information

Entry
Database: PDB / ID: 2qg6
TitleCrystal structure of human nicotinamide riboside kinase (NRK1) in complex with nicotinamide mononucleotide (NMN)
ComponentsNicotinamide riboside kinase 1
KeywordsSIGNALING PROTEIN / TRANSFERASE / NRK / nicotinamide riboside kinase / NAD+ / nucleoside monophosphate (NMP) kinase / nicotinamide mononucleotide / ADP / tiazofurin
Function / homology
Function and homology information


nicotinate riboside kinase / ribosylnicotinate kinase activity / ribosylnicotinamide kinase / ribosylnicotinamide kinase activity / Nicotinate metabolism / NAD metabolic process / NAD biosynthetic process / phosphorylation / ATP binding / metal ion binding ...nicotinate riboside kinase / ribosylnicotinate kinase activity / ribosylnicotinamide kinase / ribosylnicotinamide kinase activity / Nicotinate metabolism / NAD metabolic process / NAD biosynthetic process / phosphorylation / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
AAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / PHOSPHATE ION / Nicotinamide riboside kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsKhan, J.A. / Xiang, S. / Tong, L.
CitationJournal: Structure / Year: 2007
Title: Crystal structure of human nicotinamide riboside kinase
Authors: Khan, J.A. / Xiang, S. / Tong, L.
History
DepositionJun 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nicotinamide riboside kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9753
Polymers23,5451
Non-polymers4302
Water5,819323
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.725, 141.526, 62.091
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsThe biological unit is a monomer

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Components

#1: Protein Nicotinamide riboside kinase 1 / E.C.2.7.1.- / NRK1


Mass: 23544.654 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRK1, C9orf95 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta
References: UniProt: Q9NWW6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE


Mass: 335.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N2O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 28% (w/v) PEG 3350, 200 mM NH4Cl, 5 mM DTT, 5 mM Na2HPO, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 30, 2006
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 75133 / Num. obs: 74763 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rsym value: 0.087 / Net I/σ(I): 23.3
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.77 / Num. unique all: 7396 / Rsym value: 0.462 / % possible all: 98.2

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→30 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.206 5386 7.2 %
Rwork0.191 --
all0.191 71557 -
obs0.206 71557 95.9 %
Solvent computationBsol: 52.753 Å2
Displacement parametersBiso mean: 19.163 Å2
Baniso -1Baniso -2Baniso -3
1--2.563 Å20 Å20 Å2
2--2.032 Å20 Å2
3---0.531 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 27 323 1852
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.259
X-RAY DIFFRACTIONc_mcbond_it1.1721.5
X-RAY DIFFRACTIONc_scbond_it2.1462
X-RAY DIFFRACTIONc_mcangle_it1.9192
X-RAY DIFFRACTIONc_scangle_it3.1972.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5nmnparameter.txtnmntopo.txt

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