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- PDB-8b47: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -

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Basic information

Entry
Database: PDB / ID: 8b47
TitleCrystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a cyclic 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
Chem-OWU / PHOSPHATE ION / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 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
DepositionSep 20, 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

Downloads & links

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Assembly

Deposited unit
A: NAD kinase 1
B: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9507
Polymers62,0912
Non-polymers1,8605
Water1,18966
1
A: NAD kinase 1
B: NAD kinase 1
hetero molecules

A: NAD kinase 1
B: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,90014
Polymers124,1814
Non-polymers3,71910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area9770 Å2
ΔGint-84 kcal/mol
Surface area41410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.406, 145.885, 54.904
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 31045.279 Da / Num. of mol.: 2
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-OWU / (1~{R},23~{R},24~{S},25~{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-24,25-bis(oxidanyl)-20,20-bis(oxidanylidene)-26-oxa-20$l^{6}-thia-2,4,6,9,14,17,21-heptazatetracyclo[21.2.1.0^{2,10}.0^{3,8}]hexacosa-3,5,7,9-tetraen-11-yn-16-one


Mass: 715.698 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N13O9S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.04 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 25 %(v/v) PEG 550 MME

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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: Jul 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.53→72.94 Å / Num. obs: 17576 / % possible obs: 98.7 % / Redundancy: 12.3 % / Biso Wilson estimate: 59.07 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.218 / Rpim(I) all: 0.063 / Rrim(I) all: 0.227 / Net I/σ(I): 10.1
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
2.53-2.637.12.1341246117550.3590.8412.3050.889.6
9.1-72.9411.20.06150054480.9990.0180.06433.999.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimless0.7.7data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RG9

6rg9


Resolution: 2.53→51.39 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2588 3247 10.04 %
Rwork0.2029 29106 -
obs0.2085 17478 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.13 Å2 / Biso mean: 62.511 Å2 / Biso min: 38.54 Å2
Refinement stepCycle: final / Resolution: 2.53→51.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4134 0 148 66 4348
Biso mean--68.07 56.56 -
Num. residues----520
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.53-2.560.32031080.3061933104172
2.56-2.60.30871370.30541185132292
2.6-2.650.38781430.32051256139996
2.65-2.690.36861350.29571206134197
2.69-2.740.36441440.31631279142398
2.74-2.790.45391440.334712991443100
2.79-2.850.35681420.288212801422100
2.85-2.910.32791460.27412821428100
2.91-2.980.30431430.258912951438100
2.98-3.050.29281480.226213191467100
3.05-3.140.2791410.231112721413100
3.14-3.230.30121480.222613051453100
3.23-3.330.26011460.230312811427100
3.33-3.450.28721440.227112901434100
3.45-3.590.24221400.170812781418100
3.59-3.750.21491480.17412831431100
3.75-3.950.27161430.162213111454100
3.95-4.20.20981470.16813211468100
4.2-4.520.21011380.152312671405100
4.52-4.980.17241420.150512871429100
4.98-5.70.29921390.188413041443100
5.7-7.170.28611380.208112841422100
7.18-51.390.22071430.21021289143299
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)
14.0249-0.9277-1.18642.9001-0.41686.22790.1390.1753-0.0387-0.1024-0.0628-0.2006-0.04970.2182-0.08680.3713-0.029-0.04660.42870.0250.428523.073222.0401-6.9716
21.1015-0.1874-0.19120.3008-0.31482.8686-0.08-0.0647-0.01530.06260.0452-0.01290.18580.03740.04540.4433-0.00930.02720.3581-0.00760.551913.973615.51411.8265
36.724-4.36162.04794.8513-4.33345.09970.4485-0.0542-1.18552.7147-0.51430.7246-1.0480.2628-0.06621.0878-0.19980.05850.4862-0.0070.78285.7730.191827.3906
41.9879-0.02310.43771.5282-0.70364.60420.11170.0835-0.0178-0.0026-0.1158-0.2033-0.13950.3435-0.00490.36820.02030.02180.3114-0.00320.49714.719915.496412.198
50.565-0.00970.74391.47051.45068.92650.0226-0.21410.14390.117-0.07610.0891-0.6925-0.53050.08180.38070.04650.0350.4452-0.01640.4788-17.069123.897928.6498
62.83130.09510.70241.8827-0.92053.37180.15070.02790.0416-0.0988-0.0710.0614-0.066-0.1046-0.08210.34550.0550.02910.3187-0.02570.4587-9.336114.397713.7483
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 79 )A1 - 79
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 184 )A80 - 184
3X-RAY DIFFRACTION3chain 'A' and (resid 185 through 198 )A185 - 198
4X-RAY DIFFRACTION4chain 'A' and (resid 199 through 263 )A199 - 263
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 141 )B1 - 141
6X-RAY DIFFRACTION6chain 'B' and (resid 142 through 264 )B142 - 264

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