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- PDB-8qg6: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -

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Basic information

Entry
Database: PDB / ID: 8qg6
TitleCrystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a di-adenosine derivative
ComponentsNAD kinase 1
KeywordsTRANSFERASE / tetrameric NAD-kinase
Function / homology
Function and homology information


NAD+ kinase / NAD+ kinase activity / NADP+ biosynthetic process / NAD+ metabolic process / NAD binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
ATP-NAD kinase C-terminal domain / 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
CITRIC ACID / : / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.142 Å
AuthorsGelin, M. / Labesse, G. / Lionne, C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE18-0011-02 France
CitationJournal: To be published
Title: Crystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a di-adenosine derivative
Authors: Gelin, M. / Labesse, G. / Clement, D. / Pochet, S. / Lionne, C. / Leseigneur, C. / Huteau, V.
History
DepositionSep 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7663
Polymers31,0451
Non-polymers7212
Water1,71195
1
A: NAD kinase 1
hetero molecules

A: NAD kinase 1
hetero molecules

A: NAD kinase 1
hetero molecules

A: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,06412
Polymers124,1814
Non-polymers2,8838
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)62.800, 75.360, 118.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

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Components

#1: Protein NAD kinase 1 / ATP-dependent NAD kinase


Mass: 31045.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Gene: nadK1, lmo0968 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8Y8D7, NAD+ kinase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-V09 / (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[3-[6-azanyl-9-(phenylmethyl)purin-8-yl]prop-2-ynoxymethyl]oxolane-3,4-diol


Mass: 528.523 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H24N10O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.26 Å3/Da / Density % sol: 45.49 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 30 mM NaBr, 220 mM Kcitrate, glycerol 6%, 15-16% w/v PEG400
PH range: 4.8-5.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979288 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979288 Å / Relative weight: 1
ReflectionResolution: 2.14→63.58 Å / Num. obs: 14311 / % possible obs: 90.4 % / Redundancy: 6.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.043 / Rrim(I) all: 0.111 / Χ2: 0.86 / Net I/σ(I): 10.8 / Num. measured all: 91783
Reflection shellResolution: 2.14→2.2 Å / % possible obs: 99.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.588 / Num. measured all: 6409 / Num. unique obs: 1271 / CC1/2: 0.94 / Rpim(I) all: 0.287 / Rrim(I) all: 0.657 / Χ2: 0.49 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
Aimlessdata scaling
MOSFLMdata reduction
PHENIXphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.142→34.965 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2178 685 4.84 %
Rwork0.1939 --
obs0.1951 14151 89.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.142→34.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2046 0 52 95 2193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022193
X-RAY DIFFRACTIONf_angle_d0.7092971
X-RAY DIFFRACTIONf_dihedral_angle_d15.6891293
X-RAY DIFFRACTIONf_chiral_restr0.068323
X-RAY DIFFRACTIONf_plane_restr0.003373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1421-2.30750.33761210.3542258X-RAY DIFFRACTION77
2.3075-2.53960.26741420.2252969X-RAY DIFFRACTION100
2.5396-2.90690.29511580.22132606X-RAY DIFFRACTION88
2.9069-3.66180.22881490.19112779X-RAY DIFFRACTION94
3.6618-34.9650.15551150.16552854X-RAY DIFFRACTION93
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)
14.1965-0.8577-1.76392.94641.43575.5842-0.2488-0.84150.0230.01120.23290.3292-0.4305-0.19780.23160.51230.09490.0340.6824-0.12760.3818.908622.738228.6005
23.794-0.5339-1.48861.59940.52464.8184-0.1592-0.10480.30460.3518-0.12140.3645-0.3564-0.51890.10590.51830.11720.02120.5594-0.13260.41339.467925.783319.4576
34.0075-0.9024-1.83432.25730.92825.045-0.4512-0.60030.09020.03360.23490.0214-0.2399-0.03920.12460.51810.00240.02620.5004-0.09950.369816.722921.583317.8237
42.0323-0.7532-1.46461.17010.93575.25310.0842-1.010.79260.13690.29140.0743-1.36430.5202-0.1750.6177-0.0530.04810.8185-0.25380.520420.702428.534923.8719
52.4675-0.4278-0.18692.58720.50173.9380.05610.24890.1034-0.12350.00050.2773-0.173-0.42340.0420.25060.02680.00470.30640.03370.249918.855513.0286-3.6416
64.63980.7827-0.30585.78040.26334.6930.010.4726-0.3188-0.7026-0.11890.08870.5605-0.16350.00970.47810.0313-0.02810.43350.03440.262925.52851.2951-12.5994
73.6949-0.267-0.11242.4184-0.28824.15180.17580.71010.2703-0.1178-0.10410.5124-0.125-0.4570.06170.36310.0981-0.05150.39010.04250.323417.509515.6571-10.2655
83.9540.59741.01393.52271.28544.5998-0.0560.36430.09150.02460.03640.91010.1068-1.02460.05920.30770.1032-0.01480.5359-0.03320.45968.995813.3679-3.9744
93.6614-0.826-0.2373.16670.87543.9087-0.1705-0.63420.66270.2670.2275-0.1284-1.1663-0.08080.04590.6193-0.04630.08240.3758-0.12570.461722.857726.665514.9383
106.0666-0.296-0.27337.45440.46866.0316-0.1559-1.25390.27350.84560.1644-0.68620.01790.0865-0.0180.4709-0.05160.02460.5093-0.09580.288531.095913.133817.5024
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 79 )
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 101 )
5X-RAY DIFFRACTION5chain 'A' and (resid 102 through 184 )
6X-RAY DIFFRACTION6chain 'A' and (resid 185 through 198 )
7X-RAY DIFFRACTION7chain 'A' and (resid 199 through 216 )
8X-RAY DIFFRACTION8chain 'A' and (resid 217 through 238 )
9X-RAY DIFFRACTION9chain 'A' and (resid 239 through 252 )
10X-RAY DIFFRACTION10chain 'A' and (resid 253 through 264 )

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