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- PDB-2qt1: Human nicotinamide riboside kinase 1 in complex with nicotinamide... -

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Basic information

Entry
Database: PDB / ID: 2qt1
TitleHuman nicotinamide riboside kinase 1 in complex with nicotinamide riboside
ComponentsNicotinamide riboside kinase 1
KeywordsTRANSFERASE / non-protein kinase / NAD+ / nicotinamide riboside / nrk1 / nicotinamide riboside kinase activity / nicotinic acid riboside kinase activity / NAD biosynthesis / pyridine nucleotide biosynthesis / ADP / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / Alternative splicing / ATP-binding / Nucleotide-binding
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 / 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
Nicotinamide riboside / PHOSPHATE ION / Nicotinamide riboside kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.32 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 1.5Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: Nicotinamide riboside kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,72410
Polymers24,3731
Non-polymers3509
Water2,558142
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.529, 141.906, 62.062
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

#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
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NNR / Nicotinamide riboside / 3-(aminocarbonyl)-1-beta-D-ribofuranosylpyridinium


Mass: 255.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N2O5
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


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


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6
Details: 15% PEG 3350, 0.2M Sodium phosphate monobasic, 0.1M Bis-Tris. The protein solution (40mg/mL) contained 0.01M Nicotinamide riboside, 0.01M AMPPNP and 0.02M Magnesium chloride, pH 6.0, VAPOR ...Details: 15% PEG 3350, 0.2M Sodium phosphate monobasic, 0.1M Bis-Tris. The protein solution (40mg/mL) contained 0.01M Nicotinamide riboside, 0.01M AMPPNP and 0.02M Magnesium chloride, pH 6.0, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.32→40 Å / Num. obs: 54142 / % possible obs: 93.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.129 / Χ2: 1.775 / Net I/σ(I): 5.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.32-1.375.40.59953480.20894.3
1.37-1.425.90.45454420.21395.4
1.42-1.497.10.39755120.33796.5
1.49-1.577.40.2655240.32596.9
1.57-1.667.50.2255750.45197.3
1.66-1.797.50.18956180.66197.8
1.79-1.976.60.22947132.41381.9
1.97-2.2670.13854831.94695
2.26-2.847.30.10855883.90395.7
2.84-406.70.08453397.37988.4

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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
MAR345CCDdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2P0E

2p0e


Resolution: 1.32→36.01 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.895 / WRfactor Rfree: 0.235 / WRfactor Rwork: 0.225 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Coot, molprobity programs have also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2750 5.1 %Consistent with isomorphous data set of NRK1.ADP complex
Rwork0.242 ---
all0.243 ---
obs0.243 53951 93.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.765 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2---0.13 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.32→36.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1587 0 30 142 1759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221661
X-RAY DIFFRACTIONr_bond_other_d00.021124
X-RAY DIFFRACTIONr_angle_refined_deg1.481.9822277
X-RAY DIFFRACTIONr_angle_other_deg3.9983.0022752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.385213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.24924.73776
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.04415291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.613157
X-RAY DIFFRACTIONr_chiral_restr0.0850.2254
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021834
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02331
X-RAY DIFFRACTIONr_nbd_refined0.220.2347
X-RAY DIFFRACTIONr_nbd_other0.2290.21106
X-RAY DIFFRACTIONr_nbtor_refined0.190.2817
X-RAY DIFFRACTIONr_nbtor_other0.1120.2780
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2118
X-RAY DIFFRACTIONr_metal_ion_refined0.120.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.20.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.216
X-RAY DIFFRACTIONr_mcbond_it1.7892984
X-RAY DIFFRACTIONr_mcbond_other02389
X-RAY DIFFRACTIONr_mcangle_it2.47631621
X-RAY DIFFRACTIONr_scbond_it2.2492677
X-RAY DIFFRACTIONr_scangle_it3.0433643
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 (%)
1.32-1.3560.3642080.3323657418292.42
1.356-1.3930.3381880.323689409894.607
1.393-1.4340.3491740.3113667400096.025
1.434-1.4780.2691950.2583527388395.854
1.478-1.5260.271690.2473471375996.834
1.526-1.580.2581810.2193370366097.022
1.58-1.6390.2581730.2173256352297.359
1.639-1.7060.2411710.2173125337597.659
1.706-1.7820.2281720.2123038328297.806
1.782-1.8680.2211540.2172910312797.985
1.868-1.9690.4441080.3921814297264.67
1.969-2.0880.2281310.2142641281998.333
2.088-2.2320.2611350.232303267091.311
2.232-2.410.3481200.32081245889.544
2.41-2.6390.2111320.2012154230099.391
2.639-2.9480.2391070.2131976209299.57
2.948-3.40.19990.2141695184797.13
3.4-4.1550.199540.206942158962.681
4.155-5.8380.195520.2041188125299.042
5.838-36.0140.31270.30169776095.263

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