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

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Basic information

Entry
Database: PDB / ID: 7zza
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-KH9 / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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)31,9643
Polymers31,0451
Non-polymers9192
Water84747
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)127,85612
Polymers124,1814
Non-polymers3,6758
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 area11190 Å2
ΔGint-40 kcal/mol
Surface area39730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.840, 74.171, 118.537
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-404-

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-KH9 / 2-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[3-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-[(3-azanylpropylcarbamoylamino)methyl]-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]prop-2-ynyl]amino]ethanoic acid


Mass: 726.700 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H38N14O9 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.22 Å3/Da / Density % sol: 44.71 %
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: 2.05→37.28 Å / Num. obs: 17708 / % possible obs: 99.6 % / Redundancy: 13.1 % / Biso Wilson estimate: 43.45 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.019 / Rrim(I) all: 0.068 / Net I/σ(I): 21.4 / Num. measured all: 232119 / Scaling rejects: 21
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
2.05-2.118.91.2561154812990.8910.4411.3361.895.9
8.94-37.28110.05427742530.9930.020.05849.299

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHENIX1.19.1_4122phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RG9

6rg9


Resolution: 2.05→37.09 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2205 1768 10.02 %
Rwork0.1955 15882 -
obs0.198 17650 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.65 Å2 / Biso mean: 52.665 Å2 / Biso min: 27.52 Å2
Refinement stepCycle: final / Resolution: 2.05→37.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 65 47 2171
Biso mean--53.27 48.71 -
Num. residues----261
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.110.33261270.31041148127595
2.11-2.170.28881330.27071198133198
2.17-2.240.29871340.26641196133099
2.24-2.320.30621370.234212231360100
2.32-2.410.26991340.205412061340100
2.41-2.520.24311330.193411981331100
2.52-2.650.23751370.19381232136999
2.65-2.820.28171360.216412101346100
2.82-3.040.25841370.222912301367100
3.04-3.340.24831380.20412341372100
3.34-3.820.20121360.175612361372100
3.83-4.820.15541400.147412561396100
4.82-37.090.19731460.206313151461100
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)
14.01190.2145-2.41110.0921-0.01857.7046-0.0244-0.35060.24090.02230.05080.0315-0.45670.0238-0.02520.44540.05780.02560.4104-0.09530.409613.449524.188822.4998
21.7898-0.03290.27652.02790.35844.08350.03690.05640.1085-0.0753-0.08750.2619-0.0065-0.32830.05340.27460.03370.01090.30080.01590.328419.083513.5078-1.6822
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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