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

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Basic information

Entry
Database: PDB / ID: 7zze
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 / NADP biosynthetic process / NAD+ kinase activity / NAD metabolic process / NAD binding / phosphorylation / 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 / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / NAD kinase/diacylglycerol kinase-like domain superfamily
Similarity search - Domain/homology
CITRIC ACID / Chem-OVL / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 2.0May 24, 2023Group: Non-polymer description / Category: chem_comp / Item: _chem_comp.formula
Revision 2.1Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)31,9463
Polymers31,0451
Non-polymers9012
Water1,69394
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)127,78412
Polymers124,1814
Non-polymers3,6038
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 area11640 Å2
ΔGint-52 kcal/mol
Surface area40220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.134, 74.526, 118.438
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22

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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-OVL / (1~{R},25~{R},26~{S},27~{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-26,27-bis(oxidanyl)-28-oxa-2,4,6,9,14,17,21,23-octazatetracyclo[23.2.1.0^{2,10}.0^{3,8}]octacosa-3(8),4,6,9-tetraen-11-yne-16,22-dione


Mass: 708.685 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H36N14O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 45.18 %
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-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.78→48.17 Å / Num. obs: 47612 / % possible obs: 98.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 29.54 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.06 / Rrim(I) all: 0.125 / Net I/σ(I): 6.1
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
1.78-1.843.41.639879625970.4381.0131.9370.799.1
6.89-48.174.20.07121425140.9910.0370.08118.397.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RG9

6rg9


Resolution: 1.78→37.26 Å / SU ML: 0.275 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.7541
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2397 2370 4.98 %
Rwork0.198 45242 -
obs0.2001 47612 92.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.35 Å2
Refinement stepCycle: LAST / Resolution: 1.78→37.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 64 94 2236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01432224
X-RAY DIFFRACTIONf_angle_d1.31583015
X-RAY DIFFRACTIONf_chiral_restr0.4068323
X-RAY DIFFRACTIONf_plane_restr0.0108382
X-RAY DIFFRACTIONf_dihedral_angle_d17.3974811
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.820.46111070.39192268X-RAY DIFFRACTION78.15
1.82-1.860.40151380.38932522X-RAY DIFFRACTION88.11
1.86-1.90.36111190.36812471X-RAY DIFFRACTION85.23
1.9-1.950.32481190.32632443X-RAY DIFFRACTION84.3
1.95-20.32371520.28632540X-RAY DIFFRACTION88.2
2-2.060.27751370.25532802X-RAY DIFFRACTION97.03
2.06-2.120.28771470.24942807X-RAY DIFFRACTION96.03
2.12-2.20.27281380.23262789X-RAY DIFFRACTION96.86
2.2-2.290.26711480.23332679X-RAY DIFFRACTION93.21
2.29-2.390.24811370.21582849X-RAY DIFFRACTION97.2
2.39-2.520.21881550.20562754X-RAY DIFFRACTION96.48
2.52-2.680.26721440.20152760X-RAY DIFFRACTION94.78
2.68-2.880.22531350.19582597X-RAY DIFFRACTION89.78
2.88-3.170.26131340.18942819X-RAY DIFFRACTION96.69
3.17-3.630.25171510.16642747X-RAY DIFFRACTION95.61
3.63-4.570.20041650.14612706X-RAY DIFFRACTION94.25
4.58-37.260.18631440.16742689X-RAY DIFFRACTION92.58
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)
11.75178533989-0.309322640263-1.689306331831.571867719271.176658427556.811063636260.00821658552783-0.3242475938830.14468111830.2005928211860.04183112615760.0778897311776-0.2885166975990.036300257596-0.02481847237430.2747478673590.05715002037410.01507466111630.284400323878-0.05354015078280.25907462675513.057512612723.650327381119.1337270424
21.626069273430.09776009869920.2548175201061.605914834650.6003529817643.132125100930.0362883966313-0.006342328656770.0990945444539-0.0351715179752-0.07362606014740.198489617522-0.00138096021974-0.3267889339550.03778462761310.1865888777080.02406477407260.002143804135260.2317295909540.003671667234820.2367605074620.218676718612.8683770218-1.58097452717
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 120 )1 - 1201 - 117
22chain 'A' and (resid 121 through 264 )121 - 264118 - 261

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