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- PDB-7zz9: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -

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Basic information

Entry
Database: PDB / ID: 7zz9
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-KG6 / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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)31,9353
Polymers31,0451
Non-polymers8902
Water1,53185
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)127,74012
Polymers124,1814
Non-polymers3,5598
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 area10970 Å2
ΔGint-47 kcal/mol
Surface area40530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.991, 74.509, 118.583
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

21A-485-

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-KG6 / 3-[[(2~{R},3~{S},4~{R},5~{R})-5-[8-[3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-azanylethyl)amino]prop-1-ynyl]-6-azanyl-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-3-oxidanylidene-propanoic acid


Mass: 697.659 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H35N13O9 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.24 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: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.69→63.089 Å / Num. obs: 231225 / % possible obs: 90.1 % / Redundancy: 10.9 % / Biso Wilson estimate: 31.25 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.016 / Rrim(I) all: 0.055 / Net I/σ(I): 22.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.69-1.8263.90.599477512220.7840.3360.6921.744.7
5.15-63.08912.90.0341573412210.9990.010.03564.699.6

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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: 1.89→55.63 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2098 2201 5.24 %
Rwork0.1711 39797 -
obs0.1731 41998 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.53 Å2 / Biso mean: 42.0633 Å2 / Biso min: 21.64 Å2
Refinement stepCycle: final / Resolution: 1.89→55.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 63 85 2219
Biso mean--40.63 42.64 -
Num. residues----262
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.89-1.930.32171130.25441994210778
1.93-1.980.24761390.23472288242789
1.98-2.030.25731450.22212397254294
2.03-2.080.2921950.19362503259898
2.08-2.140.23181220.17912556267899
2.14-2.210.19741400.166825582698100
2.21-2.290.20132060.165224622668100
2.29-2.380.19861270.162825832710100
2.38-2.490.21991330.181325522685100
2.49-2.620.1941310.162125842715100
2.62-2.790.20111350.186425412676100
2.79-30.24621610.188625352696100
3-3.30.24241670.193125462713100
3.3-3.780.19071270.153725552682100
3.78-4.760.15671400.141525602700100
4.76-55.630.22951200.171825832703100
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)
12.601-0.305-1.71440.76130.77184.45540.0092-0.38220.22960.10260.0460.0567-0.31980.1233-0.0650.41050.05580.02720.4148-0.06910.340113.543924.252922.442
21.6603-0.12870.34241.64050.11412.79920.04280.02670.1133-0.0961-0.07290.2658-0.0781-0.34510.02840.2240.02860.00660.28320.00370.27519.1213.5646-1.7911
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 102 )A1 - 102
2X-RAY DIFFRACTION2chain 'A' and (resid 103 through 264 )A103 - 264

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