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- PDB-7r4j: Crystal structure of human mitochondrial NAD kinase -

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Basic information

Entry
Database: PDB / ID: 7r4j
TitleCrystal structure of human mitochondrial NAD kinase
ComponentsNAD kinase 2, mitochondrial
KeywordsTRANSFERASE / Apo-form
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 / 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
Similarity search - Domain/homology
NAD kinase 2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsLabesse, G. / Mary, C. / Gelin, M. / Lionne, C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE18-0011-01 France
CitationJournal: Mol.Cell / Year: 2022
Title: Crystal structure of human NADK2 reveals a dimeric organization and active site occlusion by lysine acetylation.
Authors: Mary, C. / Soflaee, M.H. / Kesavan, R. / Gelin, M. / Brown, H. / Zacharias, G. / Mathews, T.P. / Lemoff, A. / Lionne, C. / Labesse, G. / Hoxhaj, G.
History
DepositionFeb 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 14, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD kinase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7693
Polymers44,6891
Non-polymers802
Water37821
1
A: NAD kinase 2, mitochondrial
hetero molecules

A: NAD kinase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5396
Polymers89,3792
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3840 Å2
ΔGint-43 kcal/mol
Surface area32840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.472, 68.472, 221.615
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 44689.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NADK2, C5orf33, MNADK, NADKD1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4G0N4, NAD+ kinase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400 28% v/v, CaCl2 150 mM, 0.1 M Sodium HEPES, 2% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.95→48.42 Å / Num. obs: 20060 / % possible obs: 94.3 % / Redundancy: 2.69 % / Biso Wilson estimate: 100.84 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.121 / Rrim(I) all: 0.149 / Χ2: 0.796 / Net I/σ(I): 6.7 / Num. measured all: 53958
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.95-3.122.62.0390.468576345432980.1022.52695.5
3.12-3.342.6611.1410.888213319630860.3321.40696.6
3.34-3.612.7340.5332.037851302228720.6760.65895
3.61-3.952.6820.283.797004273726110.8890.34595.4
3.95-4.412.7260.1496.896472251523740.9710.18394.4
4.41-5.092.7160.08311.985612220720660.990.10293.6
5.09-6.212.7650.07513.174773187117260.9910.09192.3
6.21-8.712.7160.04719.673523144212970.9970.05789.9
8.71-48.422.6490.02534.3119348267300.9990.0388.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alphafold

Resolution: 2.95→48.42 Å / SU ML: 0.63 / Cross valid method: THROUGHOUT / σ(F): 1.9 / Phase error: 34.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2978 1969 9.82 %
Rwork0.2307 18088 -
obs0.2376 20057 94.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 258.45 Å2 / Biso mean: 106.5141 Å2 / Biso min: 61.88 Å2
Refinement stepCycle: final / Resolution: 2.95→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2690 0 2 21 2713
Biso mean--110.62 83.25 -
Num. residues----340
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.020.50511360.43321310144695
3.02-3.10.44081350.40391333146896
3.1-3.190.4261410.35871293143497
3.19-3.30.41471590.33461311147095
3.3-3.410.33941190.31621344146395
3.41-3.550.30611300.30391324145497
3.55-3.710.33091760.26881269144595
3.71-3.910.28971290.24081294142394
3.91-4.150.35731460.22091292143894
4.15-4.470.29931590.19511287144695
4.47-4.920.23191280.17431297142593
4.92-5.630.27961320.18651281141394
5.63-7.090.30091330.22881250138392
7.11-48.420.24361460.19461203134988
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)
15.3113-2.56170.33874.0194-2.21995.06270.92230.80670.4673-0.3730.17410.1407-0.20010.09230.00420.71630.03770.13010.86470.33750.8985-24.5099-4.174220.6152
26.44541.01260.88192.99170.08265.57820.0707-0.11680.4939-0.19610.083-0.2682-0.56870.7104-0.20520.667-0.07780.04870.775-0.01080.8484-22.5904-8.965930.3712
33.41240.79170.18452.7832.05623.6359-0.13090.09240.12510.34730.12410.2766-0.0615-0.4554-0.05680.51030.0548-0.0190.65870.11380.6515-28.095-19.024330.0654
43.17860.9404-2.28354.32950.43765.6061-0.0331-0.4860.2574-0.02620.34920.0370.47710.4265-0.19460.49490.0688-0.05430.6060.03820.7677-13.0548-26.890218.7983
52.2003-0.4645-2.52291.71721.44985.02730.2561.0061-0.4067-0.5901-0.02540.06360.45720.2207-0.06120.9667-0.0449-0.03921.1605-0.01811.1602-19.8971-32.65374.3309
60.0299-0.16820.14294.75-5.3095.9964-0.59750.89251.7826-0.9019-0.60271.80721.2065-1.2858-0.21340.6313-0.41370.20881.9078-0.32461.7032-47.8226-39.255-2.147
74.0271-0.77491.5613.58570.07563.3106-0.3030.4703-0.9449-0.39020.00350.40291.4511-1.7480.23720.9591-0.0061-0.09850.9848-0.15250.9926-31.0234-37.16128.0101
82.1572-1.2735-0.88511.30741.89814.02550.07280.4093-0.4868-0.2588-0.02510.21310.07680.0721-0.1280.63040.032-0.0980.71720.05020.9634-14.9881-30.394213.4147
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 64 through 110 )A64 - 110
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 160 )A111 - 160
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 211 )A161 - 211
4X-RAY DIFFRACTION4chain 'A' and (resid 212 through 277 )A212 - 277
5X-RAY DIFFRACTION5chain 'A' and (resid 278 through 327 )A278 - 327
6X-RAY DIFFRACTION6chain 'A' and (resid 328 through 349 )A328 - 349
7X-RAY DIFFRACTION7chain 'A' and (resid 350 through 391 )A350 - 391
8X-RAY DIFFRACTION8chain 'A' and (resid 392 through 442 )A392 - 442

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