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- PDB-7zzg: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -

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Basic information

Entry
Database: PDB / ID: 7zzg
TitleCrystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a linear 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 / Chem-KHL / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsGelin, M. / Labesse, G.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE18-0011-02 France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05-01 France
CitationJournal: Eur.J.Med.Chem. / Year: 2023
Title: Synthesis and structure-activity relationship studies of original cyclic diadenosine derivatives as nanomolar inhibitors of NAD kinase from pathogenic bacteria.
Authors: Clement, D.A. / Gelin, M. / Leseigneur, C. / Huteau, V. / Mondange, L. / Pons, J.L. / Dussurget, O. / Lionne, C. / Labesse, G. / Pochet, S.
History
DepositionMay 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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

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Assembly

Deposited unit
A: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9323
Polymers31,0451
Non-polymers8872
Water95553
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)127,72812
Polymers124,1814
Non-polymers3,5478
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 area11180 Å2
ΔGint-49 kcal/mol
Surface area41330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.383, 75.341, 119.008
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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-KHL / (1~{R},24~{R},25~{S},26~{R})-14-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-7-azanyl-25,26-bis(oxidanyl)-27-oxa-2,4,6,9,14,17,20,22-octazatetracyclo[22.2.1.0^{2,10}.0^{3,8}]heptacosa-3(8),4,6,9-tetraen-11-yne-16,21-dione


Mass: 694.659 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H34N14O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.29 Å3/Da / Density % sol: 46.25 %
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: ID23-2 / Wavelength: 0.873128 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873128 Å / Relative weight: 1
ReflectionResolution: 1.683→63.66 Å / Num. obs: 128030 / % possible obs: 90.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 36.27 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.045 / Rrim(I) all: 0.09 / Net I/σ(I): 10.7
Reflection shell

Num. unique obs: 862 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.683-1.8935.10.84544100.7210.4110.9421.975.1
5.666-63.6573.50.03130450.9990.0180.03628.390.2

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
PHENIX1.19.1_4122phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RG9

6rg9


Resolution: 2.3→63.66 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 1119 4.99 %
Rwork0.187 21327 -
obs0.189 22446 91.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.07 Å2 / Biso mean: 45.5385 Å2 / Biso min: 20.98 Å2
Refinement stepCycle: final / Resolution: 2.3→63.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 63 53 2187
Biso mean--40.33 40.36 -
Num. residues----261
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.410.28591550.25532777293295
2.41-2.530.27561630.23912700286394
2.53-2.690.31911530.21592722287594
2.69-2.90.24741410.21372716285793
2.9-3.190.25131440.19792689283393
3.19-3.650.18851370.18312681281892
3.65-4.60.1971240.15282570269488
4.6-63.660.21021020.17122472257484
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)
12.151-0.5516-2.02081.4641.17317.92720.0333-0.37670.19340.08860.0530.0527-0.36270.1958-0.08260.34570.04540.00380.3031-0.0550.370313.029723.83719.2326
22.10870.13810.24631.80230.39083.81970.00990.05830.06570.0015-0.02050.1404-0.008-0.24460.02480.17250.03310.01690.21830.00850.273120.329513.0307-1.4244
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 120 )A1 - 120
2X-RAY DIFFRACTION2chain 'A' and (resid 121 through 264 )A121 - 264

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