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- PDB-2qt0: Human nicotinamide riboside kinase 1 in complex with nicotinamide... -

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Basic information

Entry
Database: PDB / ID: 2qt0
TitleHuman nicotinamide riboside kinase 1 in complex with nicotinamide riboside and an ATP analogue
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 / ATP analogue / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Nicotinamide riboside / Nicotinamide riboside kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.92 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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 6, 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)25,1594
Polymers24,3731
Non-polymers7863
Water63135
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.025, 97.025, 44.801
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 8
Details: 35% PEG 2000 MME, 0.1M Tris-HCl. The protein solution (40mg/mL) contained 0.01M Nicotinamide riboside, 0.01M AMPPNP and 0.02M Magnesium chloride, pH 8.0, VAPOR DIFFUSION, 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: Mar 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.92→30 Å / Num. obs: 31229 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.086 / Χ2: 1.911 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.92-1.996.20.99931121.733100
1.99-2.076.30.77731411.754100
2.07-2.166.30.53831141.826100
2.16-2.286.40.43631221.918100
2.28-2.426.50.29530971.879100
2.42-2.616.50.22331401.915100
2.61-2.876.60.14731292.048100
2.87-3.286.60.0831032.052100
3.28-4.136.70.04731322.201100
4.13-306.80.03331391.758100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å27.24 Å
Translation2.5 Å27.24 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2P0E

2p0e


Resolution: 1.92→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. The Bijvoet differences were used for phasing. 2. Arp/warp, coot, prodrg, molprobity programs have also been used in refinement. 3. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 851 5.1 %RANDOM
Rwork0.209 ---
all0.211 ---
obs-16835 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.811 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.92→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1457 0 50 35 1542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221548
X-RAY DIFFRACTIONr_bond_other_d00.021031
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.9982112
X-RAY DIFFRACTIONr_angle_other_deg4.1463.0042486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8115181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.84124.36671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37515254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.315157
X-RAY DIFFRACTIONr_chiral_restr0.0830.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021673
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02311
X-RAY DIFFRACTIONr_nbd_refined0.2070.2284
X-RAY DIFFRACTIONr_nbd_other0.2350.2918
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2750
X-RAY DIFFRACTIONr_nbtor_other0.1230.2681
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.249
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4090.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3230.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.22
X-RAY DIFFRACTIONr_mcbond_it2.3492899
X-RAY DIFFRACTIONr_mcbond_other02359
X-RAY DIFFRACTIONr_mcangle_it3.34831464
X-RAY DIFFRACTIONr_scbond_it2.4082649
X-RAY DIFFRACTIONr_scangle_it3.153646
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 (%)
1.92-1.9710.312600.2451165122899.756
1.971-2.0250.349700.2491114118699.831
2.025-2.0830.278570.2311068112699.911
2.083-2.1470.251640.21910821146100
2.147-2.2170.29460.2281045109299.908
2.217-2.2940.237450.249901035100
2.294-2.380.237540.21971102799.805
2.38-2.4770.264530.223939992100
2.477-2.5860.287630.221872935100
2.586-2.7110.295440.24862906100
2.711-2.8570.259450.248832877100
2.857-3.0280.27350.2378582199.878
3.028-3.2350.274310.22975678899.873
3.235-3.4910.294380.20968472499.724
3.491-3.8190.195340.186644678100
3.819-4.2610.212320.17458762099.839
4.261-4.9040.138240.15652655199.819
4.904-5.9660.178240.178455479100
5.966-8.2760.26170.229369386100
8.276-300.221150.203238253100

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