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

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Basic information

Entry
Database: PDB / ID: 8qgl
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: 1.83 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)31,9143
Polymers31,0451
Non-polymers8692
Water1,946108
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)127,65612
Polymers124,1814
Non-polymers3,4758
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
Buried area10840 Å2
ΔGint-48 kcal/mol
Surface area40070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.860, 74.700, 118.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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-UUC / (2~{R},3~{R},4~{S},5~{R})-2-[8-[3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy]prop-1-ynyl]-6-azanyl-purin-9-yl]-5-[[[1,1-bis(oxidanyl)-1$l^{6}-thia-3-azabicyclo[1.1.0]butan-1-yl]amino]methyl]oxolane-3,4-diol


Mass: 676.662 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H32N12O9S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
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: ID29 / Wavelength: 0.979316 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979316 Å / Relative weight: 1
ReflectionResolution: 1.83→59.26 Å / Num. obs: 24849 / % possible obs: 99.5 % / Redundancy: 6.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.045 / Rrim(I) all: 0.117 / Χ2: 0.95 / Net I/σ(I): 8.6 / Num. measured all: 159893
Reflection shellResolution: 1.83→1.87 Å / % possible obs: 99.3 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.786 / Num. measured all: 8481 / Num. unique obs: 1509 / CC1/2: 0.76 / Rpim(I) all: 0.356 / Rrim(I) all: 0.866 / Χ2: 0.94 / Net I/σ(I) obs: 2

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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: 1.83→55.534 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2161 1193 4.81 %
Rwork0.1863 --
obs0.1878 24821 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.83→55.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2062 0 60 109 2231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132217
X-RAY DIFFRACTIONf_angle_d1.0473012
X-RAY DIFFRACTIONf_dihedral_angle_d18.0171300
X-RAY DIFFRACTIONf_chiral_restr0.088329
X-RAY DIFFRACTIONf_plane_restr0.005379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.83-1.90330.3281030.29782581X-RAY DIFFRACTION99
1.9033-1.98990.32921240.26752596X-RAY DIFFRACTION99
1.9899-2.09480.25771310.21112619X-RAY DIFFRACTION100
2.0948-2.22610.24421080.19462601X-RAY DIFFRACTION99
2.2261-2.39790.27141440.20282604X-RAY DIFFRACTION99
2.3979-2.63930.25421340.18082613X-RAY DIFFRACTION100
2.6393-3.02110.22141370.18772618X-RAY DIFFRACTION99
3.0211-3.80620.19441430.17072654X-RAY DIFFRACTION100
3.8062-55.5340.17811690.16382742X-RAY DIFFRACTION99
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)
12.2707-0.2347-1.05781.44161.41764.04-0.077-0.28620.17250.0466-0.00130.1049-0.3322-0.03570.08590.37640.08440.0360.3555-0.08980.281712.427323.498623.1021
22.7352-0.4773-1.05682.6-0.95472.32260.3469-0.00490.52210.0555-0.21350.4182-0.5241-0.3320.30660.26030.09140.04370.2644-0.02990.290614.46424.26194.775
31.9283-0.05520.20532.12250.11483.08240.02370.17150.0518-0.1885-0.04890.17190.0713-0.19750.01730.12650.0285-0.01780.16970.00160.177720.922710.5885-6.566
41.9422-0.47380.31931.52460.05112.38210.003-0.08930.19290.0861-0.02630.2007-0.1953-0.29440.04640.20190.0250.04560.1908-0.0390.247818.801417.16667.2275
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 90 )
2X-RAY DIFFRACTION2chain 'A' and (resid 91 through 122 )
3X-RAY DIFFRACTION3chain 'A' and (resid 123 through 216 )
4X-RAY DIFFRACTION4chain 'A' and (resid 217 through 264 )

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