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- PDB-2ql6: human nicotinamide riboside kinase (NRK1) -

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Basic information

Entry
Database: PDB / ID: 2ql6
Titlehuman nicotinamide riboside kinase (NRK1)
Componentsnicotinamide riboside kinase 1
KeywordsSIGNALING PROTEIN / TRANSFERASE / nicotinamide riboside kinase / NRK / monophosphate (NMP) kinase / nicotinamide mononucleotide / tiazofurin / ADP
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 / cytosol / cytoplasm
Similarity search - Function
AAA domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-TIZ / Nicotinamide riboside kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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
DepositionJul 12, 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

Downloads & links

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Assembly

Deposited unit
A: nicotinamide riboside kinase 1
B: nicotinamide riboside kinase 1
C: nicotinamide riboside kinase 1
D: nicotinamide riboside kinase 1
E: nicotinamide riboside kinase 1
F: nicotinamide riboside kinase 1
G: nicotinamide riboside kinase 1
H: nicotinamide riboside kinase 1
I: nicotinamide riboside kinase 1
J: nicotinamide riboside kinase 1
K: nicotinamide riboside kinase 1
L: nicotinamide riboside kinase 1
M: nicotinamide riboside kinase 1
N: nicotinamide riboside kinase 1
O: nicotinamide riboside kinase 1
P: nicotinamide riboside kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)387,71448
Polymers376,71416
Non-polymers10,99932
Water0
1
A: nicotinamide riboside kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2323
Polymers23,5451
Non-polymers6872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: nicotinamide riboside kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2323
Polymers23,5451
Non-polymers6872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: nicotinamide riboside kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2323
Polymers23,5451
Non-polymers6872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: nicotinamide riboside kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2323
Polymers23,5451
Non-polymers6872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: nicotinamide riboside kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2323
Polymers23,5451
Non-polymers6872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: nicotinamide riboside kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2323
Polymers23,5451
Non-polymers6872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: nicotinamide riboside kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2323
Polymers23,5451
Non-polymers6872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: nicotinamide riboside kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2323
Polymers23,5451
Non-polymers6872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: nicotinamide riboside kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2323
Polymers23,5451
Non-polymers6872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: nicotinamide riboside kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2323
Polymers23,5451
Non-polymers6872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: nicotinamide riboside kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2323
Polymers23,5451
Non-polymers6872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: nicotinamide riboside kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2323
Polymers23,5451
Non-polymers6872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
M: nicotinamide riboside kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2323
Polymers23,5451
Non-polymers6872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
N: nicotinamide riboside kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2323
Polymers23,5451
Non-polymers6872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
O: nicotinamide riboside kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2323
Polymers23,5451
Non-polymers6872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
P: nicotinamide riboside kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2323
Polymers23,5451
Non-polymers6872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.710, 99.960, 145.590
Angle α, β, γ (deg.)90.000, 91.570, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 23544.654 Da / Num. of mol.: 16
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): BL21 Rossetta (DE3)
References: UniProt: Q9NWW6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-TIZ / (1R)-1-[4-(AMINOCARBONYL)-1,3-THIAZOL-2-YL]-1,4-ANHYDRO-D-RIBITOL / TIAZOFURIN / Tiazofurin


Mass: 260.267 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C9H12N2O5S / Comment: inhibitor*YM

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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: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 8% (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: X29A / Wavelength: 1.0808 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2007
Details: Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0808 Å / Relative weight: 1
Reflection twinType: hemihedral / Operator: l,-k,h / Fraction: 0.37
ReflectionResolution: 2.7→30 Å / Num. all: 122787 / Num. obs: 116539 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 13.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.98 / Num. unique all: 12243 / Rsym value: 0.28 / % possible all: 74.3

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
DENZOpackagedata reduction
SCALEPACKpackagedata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 5215 4.5 %random
Rwork0.207 ---
all0.207 108172 --
obs0.207 108172 94.1 %-
Solvent computationBsol: 10 Å2
Displacement parametersBiso mean: 21.697 Å2
Baniso -1Baniso -2Baniso -3
1--2.404 Å20 Å2-0.484 Å2
2--8.527 Å20 Å2
3----6.123 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23712 0 704 0 24416
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_scbond_it02
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scangle_it02.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2adp_tzf.param

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