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- PDB-2qsz: Human nicotinamide riboside kinase 1 in complex with nicotinamide... -

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Basic information

Entry
Database: PDB / ID: 2qsz
TitleHuman nicotinamide riboside kinase 1 in complex with nicotinamide mononucleotide
ComponentsNicotinamide riboside kinase 1
KeywordsTRANSFERASE / non-protein kinase / NAD+ / nicotinamide riboside / nrk1 / nicotinamide riboside kinase activity / nicotinic acid riboside kinase activity / NAD biosynthesis / ADP / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / Alternative splicing / ATP-binding / Nucleotide-binding / Pyridine nucleotide biosynthesis
Function / homology
Function and homology information


nicotinate riboside kinase / : / nicotinate riboside kinase activity / ribosylnicotinamide kinase / ribosylnicotinamide kinase activity / Nicotinate metabolism / NAD+ metabolic process / NAD+ biosynthetic process / ATP binding / metal ion binding ...nicotinate riboside kinase / : / nicotinate riboside kinase activity / ribosylnicotinamide kinase / ribosylnicotinamide kinase activity / Nicotinate metabolism / NAD+ metabolic process / NAD+ biosynthetic process / ATP binding / metal ion binding / cytosol / cytoplasm
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsRabeh, W.M. / Tempel, W. / Nedyalkova, L. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Brenner, C. ...Rabeh, W.M. / Tempel, W. / Nedyalkova, L. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Brenner, C. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: Plos Biol. / Year: 2007
Title: Nicotinamide Riboside Kinase Structures Reveal New Pathways to NAD(+).
Authors: Tempel, W. / Rabeh, W.M. / Bogan, K.L. / Belenky, P. / Wojcik, M. / Seidle, H.F. / Nedyalkova, L. / Yang, T. / Sauve, A.A. / Park, H.W. / Brenner, C.
History
DepositionJul 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE IS UNKNOWN.

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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)24,83911
Polymers24,3731
Non-polymers46610
Water1,856103
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.921, 142.342, 62.434
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Detailsnot known

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Nicotinamide riboside kinase 1


Mass: 24373.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRK1, C9orf95 / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL
References: UniProt: Q9NWW6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor

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Non-polymers , 5 types, 113 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE


Mass: 335.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N2O8P
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 7 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 51.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 3350, 0.2M Sodium phosphate monobasic, 0.15M D(+)sucrose, 0.1M HEPES pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 26, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 19738 / % possible obs: 99.1 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.138 / Χ2: 1.911 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.974.20.90119061.19198.1
1.97-2.054.50.74919291.30298.8
2.05-2.144.80.57619571.47698.8
2.14-2.254.80.44119451.56399.1
2.25-2.394.80.3719651.70499.5
2.39-2.584.90.27119551.76299.6
2.58-2.844.90.20719951.97499.8
2.84-3.2550.13620002.46100
3.25-4.0950.09220023.11699.4
4.09-3050.06120842.20897.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT2data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2QSY

2qsy


Resolution: 1.9→23.64 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.218 / WRfactor Rwork: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Prodrg, arp/warp, coot, molprobity programs have also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1031 5.2 %Reflections from isomorphous data of NRK1-ADP complex
Rwork0.217 ---
all0.219 ---
obs-19721 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.061 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.28 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.9→23.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1559 0 35 103 1697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221629
X-RAY DIFFRACTIONr_bond_other_d00.021108
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.9822220
X-RAY DIFFRACTIONr_angle_other_deg4.1193.0022694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7575196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.62524.54577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25515284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.199158
X-RAY DIFFRACTIONr_chiral_restr0.0790.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021776
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02326
X-RAY DIFFRACTIONr_nbd_refined0.1960.2299
X-RAY DIFFRACTIONr_nbd_other0.2280.21006
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2748
X-RAY DIFFRACTIONr_nbtor_other0.1080.2673
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.277
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1680.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.29
X-RAY DIFFRACTIONr_mcbond_it2.0692955
X-RAY DIFFRACTIONr_mcbond_other02379
X-RAY DIFFRACTIONr_mcangle_it2.8431566
X-RAY DIFFRACTIONr_scbond_it2.1562674
X-RAY DIFFRACTIONr_scangle_it2.9053649
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.9510.371760.2941237145090.552
1.951-2.0040.456750.3151328141699.082
2.004-2.0620.341700.261275135998.97
2.062-2.1250.277610.2421254133098.872
2.125-2.1940.25740.2471215130398.926
2.194-2.270.344600.2651173124399.195
2.27-2.3550.396640.2421153122599.347
2.355-2.450.266600.2261111117599.66
2.45-2.5580.26650.2061062113099.735
2.558-2.6810.276620.2111005106899.906
2.681-2.8240.276570.2129871044100
2.824-2.9930.209560.20791597299.897
2.993-3.1960.218560.214862918100
3.196-3.4470.253400.21482086299.768
3.447-3.7680.231330.22175679898.872
3.768-4.1990.185440.18367773498.229
4.199-4.8230.212300.15560164697.678
4.823-5.8470.178210.1954056898.768
5.847-8.0270.2180.23943645998.911
8.027-23.6360.29690.20228329499.32

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