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- PDB-7n29: Structure of NAD kinase -

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Basic information

Entry
Database: PDB / ID: 7n29
TitleStructure of NAD kinase
ComponentsNAD kinase 2, mitochondrial
KeywordsTRANSFERASE / NAD / ATP / kinase / mitochondria
Function / homology
Function and homology information


NAD+ kinase / NAD+ kinase activity / NADP+ biosynthetic process / Nicotinate metabolism / NAD+ metabolic process / Mitochondrial protein degradation / mitochondrial matrix / protein homodimerization activity / mitochondrion / ATP binding
Similarity search - Function
NAD kinase 2, mitochondrial / Probable inorganic polyphosphate/atp-NAD kinase; domain 1 / NAD kinase / ATP-NAD kinase, PpnK-type, C-terminal / ATP-NAD kinase N-terminal domain / NAD kinase/diacylglycerol kinase-like domain superfamily / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD kinase 2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsDu, J. / Estrella, M.A. / Jeffrey, P.D. / Korennykh, A.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM110161 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Structure of human NADK2 reveals atypical assembly and regulation of NAD kinases from animal mitochondria.
Authors: Du, J. / Estrella, M. / Solorio-Kirpichyan, K. / Jeffrey, P.D. / Korennykh, A.
History
DepositionMay 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD kinase 2, mitochondrial
B: NAD kinase 2, mitochondrial
C: NAD kinase 2, mitochondrial
D: NAD kinase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,9038
Polymers181,2504
Non-polymers2,6544
Water3,639202
1
A: NAD kinase 2, mitochondrial
hetero molecules

A: NAD kinase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9524
Polymers90,6252
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5560 Å2
ΔGint-21 kcal/mol
Surface area28500 Å2
MethodPISA
2
B: NAD kinase 2, mitochondrial
hetero molecules

C: NAD kinase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9524
Polymers90,6252
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x+1/2,-y+1/2,-z1
Buried area6020 Å2
ΔGint-25 kcal/mol
Surface area30830 Å2
MethodPISA
3
D: NAD kinase 2, mitochondrial
hetero molecules

D: NAD kinase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9524
Polymers90,6252
Non-polymers1,3272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4340 Å2
ΔGint-15 kcal/mol
Surface area29580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.129, 185.115, 188.634
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(CHAIN A AND (RESID 58 THROUGH 241 OR RESID 266...
21(CHAIN B AND (RESID 58 THROUGH 85 OR (RESID 108...
31(CHAIN C AND (RESID 58 THROUGH 85 OR (RESID 108...
41(CHAIN D AND (RESID 58 THROUGH 85 OR RESID 108 THROUGH 342 OR RESID 352 THROUGH 441 OR RESID 545))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(CHAIN A AND (RESID 58 THROUGH 241 OR RESID 266...A58
121(CHAIN A AND (RESID 58 THROUGH 241 OR RESID 266...A266
131(CHAIN A AND (RESID 58 THROUGH 241 OR RESID 266...A288
141(CHAIN A AND (RESID 58 THROUGH 241 OR RESID 266...A0
151(CHAIN A AND (RESID 58 THROUGH 241 OR RESID 266...A57 - 442
161(CHAIN A AND (RESID 58 THROUGH 241 OR RESID 266...A57 - 442
171(CHAIN A AND (RESID 58 THROUGH 241 OR RESID 266...A57 - 442
181(CHAIN A AND (RESID 58 THROUGH 241 OR RESID 266...A57 - 442
191(CHAIN A AND (RESID 58 THROUGH 241 OR RESID 266...A57 - 442
211(CHAIN B AND (RESID 58 THROUGH 85 OR (RESID 108...B58
221(CHAIN B AND (RESID 58 THROUGH 85 OR (RESID 108...B108
231(CHAIN B AND (RESID 58 THROUGH 85 OR (RESID 108...B56 - 441
241(CHAIN B AND (RESID 58 THROUGH 85 OR (RESID 108...B56 - 441
251(CHAIN B AND (RESID 58 THROUGH 85 OR (RESID 108...B56 - 441
261(CHAIN B AND (RESID 58 THROUGH 85 OR (RESID 108...B56 - 441
311(CHAIN C AND (RESID 58 THROUGH 85 OR (RESID 108...C58
321(CHAIN C AND (RESID 58 THROUGH 85 OR (RESID 108...C108
331(CHAIN C AND (RESID 58 THROUGH 85 OR (RESID 108...C58 - 441
341(CHAIN C AND (RESID 58 THROUGH 85 OR (RESID 108...C58 - 441
351(CHAIN C AND (RESID 58 THROUGH 85 OR (RESID 108...C58 - 441
361(CHAIN C AND (RESID 58 THROUGH 85 OR (RESID 108...C58 - 441
411(CHAIN D AND (RESID 58 THROUGH 85 OR RESID 108 THROUGH 342 OR RESID 352 THROUGH 441 OR RESID 545))D58
421(CHAIN D AND (RESID 58 THROUGH 85 OR RESID 108 THROUGH 342 OR RESID 352 THROUGH 441 OR RESID 545))D108
431(CHAIN D AND (RESID 58 THROUGH 85 OR RESID 108 THROUGH 342 OR RESID 352 THROUGH 441 OR RESID 545))D352
441(CHAIN D AND (RESID 58 THROUGH 85 OR RESID 108 THROUGH 342 OR RESID 352 THROUGH 441 OR RESID 545))D545

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Components

#1: Protein
NAD kinase 2, mitochondrial / Mitochondrial NAD kinase / NAD kinase domain-containing protein 1 / mitochondrial


Mass: 45312.387 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NADK2, C5orf33, MNADK, NADKD1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4G0N4, NAD+ kinase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.34 Å3/Da / Density % sol: 47.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Magnesium Chloride, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→29.79 Å / Num. obs: 42223 / % possible obs: 99.9 % / Redundancy: 14 % / CC1/2: 0.997 / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.052 / Rrim(I) all: 0.195 / Net I/σ(I): 13.9 / Num. measured all: 591288 / Scaling rejects: 1
Reflection shellResolution: 2.8→2.91 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.909 / Num. measured all: 64868 / Num. unique obs: 4427 / CC1/2: 0.932 / Rpim(I) all: 0.245 / Rrim(I) all: 0.942 / Net I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
Aimless0.7.4data scaling
SHELXCDphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.8→29.79 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 2021 4.79 %
Rwork0.191 40156 -
obs0.193 42177 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 230.84 Å2 / Biso mean: 53.4 Å2 / Biso min: 13.16 Å2
Refinement stepCycle: final / Resolution: 2.8→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10490 0 176 202 10868
Biso mean--51.85 40.15 -
Num. residues----1340
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A6112X-RAY DIFFRACTIONPOSITIONAL0
12B6112X-RAY DIFFRACTIONPOSITIONAL0
13C6112X-RAY DIFFRACTIONPOSITIONAL0
14D6112X-RAY DIFFRACTIONPOSITIONAL0
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.8-2.870.26291220.194428622984
2.87-2.950.29851420.19428342976
2.95-3.030.26671340.198328552989
3.03-3.130.25831420.187428352977
3.13-3.240.25691270.195928442971
3.24-3.370.25341340.184628642998
3.37-3.530.26441530.178128202973
3.53-3.710.23941400.169428733013
3.71-3.940.22861530.167628392992
3.94-4.250.24051460.166728553001
4.25-4.670.20711580.147228673025
4.67-5.350.23121790.170828503029
5.35-6.720.23771360.222529413077
6.73-29.790.29841550.265930173172
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9105-0.7825-1.24425.91881.35635.8079-0.42280.0858-0.45050.01040.17450.811.32210.56950.24970.8833-0.00150.14080.41580.0320.382444.9099-6.76230.4821
22.27970.9224-0.94551.7341-0.6284.1846-0.1264-0.4522-0.20580.0659-0.03090.02910.73260.17530.11470.4720.09580.0390.2707-0.03580.260248.46562.653328.9056
32.6137-0.6513-0.37082.98540.08744.62390.0450.3081-0.0483-0.1217-0.11230.2782-0.2838-0.24080.0680.1823-0.0069-0.02840.1561-0.04250.210250.033410.13565.5653
44.1871-1.9683-1.51294.96512.37292.5981-0.2388-0.0015-0.4049-0.11270.2327-0.76290.61551.51840.15510.32090.18150.12850.81770.00520.612776.6906-3.65423.3029
52.7155-0.61-0.36732.60660.17864.94390.00540.10620.2112-0.0825-0.09430.0074-0.38180.14690.07610.2519-0.02090.00560.1256-0.0280.266553.021612.338510.1382
64.53860.9439-0.68964.01150.05385.5444-0.06950.12520.1889-0.37530.3681-0.3453-0.06890.4157-0.17540.2084-0.03030.01010.3824-0.03590.255781.740745.552712.1325
71.8424-0.35030.28371.254-0.28313.1379-0.0230.1659-0.0273-0.20140.06940.1117-0.025-0.0654-0.04950.1544-0.06570.00390.20850.03090.271164.106243.4168-2.6749
83.5888-0.1801-0.18116.8557-2.36935.81390.0070.24090.6192-1.17290.1741-0.0240.0996-0.1462-0.14640.47280.0303-0.02510.72430.05760.297624.926456.180940.3626
92.6697-0.2147-0.84336.9612-0.26075.8830.2499-0.08950.4148-0.2201-0.16050.2353-0.6641-0.1351-0.07470.30620.0539-0.04510.60240.03730.246523.889451.808744.7145
102.32960.5005-0.07242.0243-0.65372.91750.1385-0.0139-0.1267-0.2758-0.1915-0.3470.22460.56980.01240.32160.16560.03640.40720.07420.313229.977437.718324.3385
111.7458-1.1861.64155.72280.28967.8497-0.2191-0.78320.0744-0.3654-0.19990.45160.2173-1.07870.27510.3437-0.07540.04660.61360.09710.3583-0.958533.51716.3446
121.62750.4554-0.27531.1093-0.17563.3258-0.010.011-0.1745-0.2584-0.1319-0.3160.5590.55010.11640.35860.19450.0420.45740.07240.347329.259234.953425.0574
136.95432.39340.35642.2045-0.43071.5711-0.3624-0.0687-0.4098-0.3923-0.0671-0.33790.30810.54670.40970.35110.15210.09090.40350.07690.284656.898988.460717.6206
142.0779-0.1850.4221.90471.22451.74610.17330.36240.0431-0.72590.34910.03640.24230.3255-0.22550.64230.2346-0.12510.49740.06560.167148.698588.338410.54
151.65261.5750.09322.10120.11091.2747-0.08860.7946-0.586-0.31190.21630.0170.0585-0.11380.0623-0.00630.02770.21290.3106-0.10880.524262.653985.837620.2652
160.54491.29440.43683.15240.58842.5708-0.47680.48860.0173-0.40940.02460.5542-0.3979-0.27210.0850.3414-0.0943-0.05850.46810.10370.440156.085599.367412.7749
171.54751.2588-1.9232.6219-1.42812.5949-0.13310.0249-0.0738-0.07520.5172-0.20270.43290.3003-0.33070.16960.05390.00280.4-0.18190.577165.14188.645234.1017
180.3063-0.37070.22520.85840.01240.37220.1983-0.5403-0.22910.41050.32130.23540.3471-1.094-0.20720.251-0.06850.12140.88570.03220.58561.210494.572352.361
191.0562-0.8638-0.34670.79110.51461.2273-0.0870.0826-0.6143-0.01690.1683-0.08430.36110.58240.0683-0.21580.24460.2217-0.02440.01610.420549.5527111.201641.8224
200.8449-0.48351.9232.74270.86387.0003-0.50140.22240.0413-0.1940.23550.33680.1705-0.48170.1650.0832-0.10670.00050.10370.02420.628160.3714102.643841.8021
211.24041.1081-2.66492.7383-3.57226.5224-0.47140.2387-0.50420.26790.0787-0.11270.10440.1440.38270.32060.14010.00990.819-0.19980.447262.515393.51149.8178
222.71093.1217-2.44563.9169-4.27198.5781-0.1233-0.2379-0.6788-0.06220.0208-0.250.1660.0880.10730.22210.04170.05750.3534-0.02990.656264.395890.761836.6378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 57 THROUGH 132 )A0
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 133 THROUGH 228 )A0
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 229 THROUGH 327 )A0
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 328 THROUGH 364 )A0
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 365 THROUGH 442 )A0
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 56 THROUGH 195 )B0
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 196 THROUGH 441 )B0
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 58 THROUGH 107 )C0
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 108 THROUGH 211 )C0
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 212 THROUGH 327 )C0
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 328 THROUGH 364 )C0
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 365 THROUGH 441 )C0
13X-RAY DIFFRACTION13CHAIN 'D' AND (RESID 58 THROUGH 107 )D0
14X-RAY DIFFRACTION14CHAIN 'D' AND (RESID 108 THROUGH 132 )D0
15X-RAY DIFFRACTION15CHAIN 'D' AND (RESID 133 THROUGH 182 )D0
16X-RAY DIFFRACTION16CHAIN 'D' AND (RESID 183 THROUGH 211 )D0
17X-RAY DIFFRACTION17CHAIN 'D' AND (RESID 212 THROUGH 276 )D0
18X-RAY DIFFRACTION18CHAIN 'D' AND (RESID 277 THROUGH 305 )D0
19X-RAY DIFFRACTION19CHAIN 'D' AND (RESID 306 THROUGH 364 )D0
20X-RAY DIFFRACTION20CHAIN 'D' AND (RESID 365 THROUGH 391 )D0
21X-RAY DIFFRACTION21CHAIN 'D' AND (RESID 392 THROUGH 407 )D0
22X-RAY DIFFRACTION22CHAIN 'D' AND (RESID 408 THROUGH 442 )D0

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