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- PDB-5dhs: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -

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Basic information

Entry
Database: PDB / ID: 5dhs
TitleCrystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a novel inhibitor
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
Probable inorganic polyphosphate/atp-NAD kinase; domain 1 / Probable inorganic polyphosphate/atp-NAD kinase; domain 2 / 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 / Tumour Suppressor Smad4 / Sandwich ...Probable inorganic polyphosphate/atp-NAD kinase; domain 1 / Probable inorganic polyphosphate/atp-NAD kinase; domain 2 / 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 / Tumour Suppressor Smad4 / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-5AG / CITRIC ACID / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsGelin, M. / Paoletti, J. / Assairi, L. / Huteau, V. / Pochet, S. / Labesse, G.
CitationJournal: Eur.J.Med.Chem. / Year: 2016
Title: 8-Thioalkyl-adenosine derivatives inhibit Listeria monocytogenes NAD kinase through a novel binding mode.
Authors: Paoletti, J. / Assairi, L. / Gelin, M. / Huteau, V. / Nahori, M.A. / Dussurget, O. / Labesse, G. / Pochet, S.
History
DepositionAug 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)126,69611
Polymers124,1814
Non-polymers2,5157
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10660 Å2
ΔGint-45 kcal/mol
Surface area40890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.770, 118.950, 66.900
Angle α, β, γ (deg.)90.000, 100.140, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1METMETASPASPchain AAA1 - 2641 - 264
2METMETHISHISchain BBB1 - 2671 - 267
3METMETGLUGLUchain CCC1 - 2631 - 263
4LYSLYSGLUGLUchain DDD2 - 2632 - 263

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Components

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


Mass: 31045.279 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Gene: nadK1, lmo0968 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y8D7, NAD+ kinase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-5AG / 5'-azido-5'-deoxy-8-[(2-{[2-(3-ethynylphenyl)ethyl]amino}-2-oxoethyl)sulfanyl]adenosine


Mass: 509.541 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H23N9O4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 30 mM sodium bromide, 220 mM potassium citrate, pH 4.8-5.1, glycerol 6%, 15-16% w/v polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.62→65.855 Å / Num. all: 30967 / Num. obs: 30967 / % possible obs: 100 % / Redundancy: 2.6 % / Biso Wilson estimate: 49.1 Å2 / Rpim(I) all: 0.039 / Rrim(I) all: 0.063 / Rsym value: 0.045 / Net I/av σ(I): 12.759 / Net I/σ(I): 12.5 / Num. measured all: 80726
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.62-2.762.70.3512.21203444920.3020.3511.9100
2.76-2.932.70.25431138042810.2240.2542.6100
2.93-3.132.60.1525.11050939880.1350.1524.2100
3.13-3.382.60.0888.6971737510.0780.0887.2100
3.38-3.712.60.04716.2885134440.040.04712.8100
3.71-4.142.60.0323.8807731100.0260.0318.5100
4.14-4.782.60.0224.2724827620.0170.0226.1100
4.78-5.862.60.0232.5592423160.0170.0226.9100
5.86-8.292.50.02127.5454818140.0180.02128.599.9
8.29-44.1392.40.01917243810090.0170.01936.699.2

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2i1w

2i1w


Resolution: 2.62→44.139 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 0.18 / Phase error: 32.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2776 1910 3.14 %
Rwork0.2425 58876 -
obs0.2437 30967 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 210.2 Å2 / Biso mean: 73.6062 Å2 / Biso min: 13.11 Å2
Refinement stepCycle: final / Resolution: 2.62→44.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8071 0 176 173 8420
Biso mean--59.54 46.43 -
Num. residues----1030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058449
X-RAY DIFFRACTIONf_angle_d0.75611437
X-RAY DIFFRACTIONf_chiral_restr0.0291247
X-RAY DIFFRACTIONf_plane_restr0.0021456
X-RAY DIFFRACTIONf_dihedral_angle_d11.7483024
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4709X-RAY DIFFRACTION11.296TORSIONAL
12B4709X-RAY DIFFRACTION11.296TORSIONAL
13C4709X-RAY DIFFRACTION11.296TORSIONAL
14D4709X-RAY DIFFRACTION11.296TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.62-2.68550.42591370.44193433099
2.6855-2.75810.42671170.38134195431299
2.7581-2.83930.40121290.372642394368100
2.8393-2.93090.36391250.351141894314100
2.9309-3.03560.40911450.325342184363100
3.0356-3.15710.29421490.297841784327100
3.1571-3.30080.3051300.271342154345100
3.3008-3.47470.28051670.245541744341100
3.4747-3.69240.24391450.216142364381100
3.6924-3.97730.23131200.21742294349100
3.9773-4.37720.26261550.188741614316100
4.3772-5.00980.2081340.176342164350100
5.0098-6.30890.24651340.214642054339100
6.3089-44.14510.26791230.2342284351100
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)
13.47821.0397-1.28695.2761-2.11443.34970.2078-0.4172-0.56330.7735-0.4101-0.1010.27810.15030.16580.7253-0.1243-0.00980.32950.03460.42315.289-30.4644-25.9485
22.94531.8091-0.93213.4345-0.79653.22280.2073-0.07850.02870.4775-0.14720.232-0.0788-0.2345-0.07770.3077-0.01560.01080.216-0.05430.26619.8662-6.4075-38.457
33.53051.31160.78731.47810.70171.66230.9553-1.38431.23540.5888-0.174-0.0905-0.70890.301-0.11210.9758-0.8084-0.01821.1046-0.30880.862535.367117.9311-23.777
43.06460.1444-0.180.96530.1833.34230.1911-0.4697-0.42390.4214-0.1606-0.78320.00350.9081-0.07580.4086-0.1182-0.21450.61080.14660.737534.4519-6.7894-33.6573
53.9247-0.4922.21432.8913-1.54133.65190.32540.77110.9139-0.9479-0.03410.5216-1.0093-0.6443-0.13690.91790.35090.07050.95060.32220.78816.12348.505-77.2942
64.13070.886-0.56973.66580.08233.13110.11680.7879-0.2977-0.2398-0.0782-0.03460.101-0.2288-0.00880.380.1885-0.01590.5-0.09230.303415.5584-12.9741-64.4097
78.3301-3.1039-3.613.63462.88114.77720.130.7657-0.6874-0.1164-0.55060.11560.75860.42520.2240.66240.37390.01621.2479-0.0830.810351.4171-23.9281-68.3525
82.13980.0788-0.09622.89230.52192.30370.2160.52870.1171-0.1398-0.1243-0.9128-0.10930.6774-0.20040.29980.10930.0850.66030.11490.59338.1317-3.2113-60.7062
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:100)A1 - 100
2X-RAY DIFFRACTION2(chain A and resid 101:264)A101 - 264
3X-RAY DIFFRACTION3(chain B and resid 1:100)B1 - 100
4X-RAY DIFFRACTION4(chain B and resid 101:264)B101 - 264
5X-RAY DIFFRACTION5(chain C and resid 1:100)C1 - 100
6X-RAY DIFFRACTION6(chain C and resid 101:264)C101 - 264
7X-RAY DIFFRACTION7(chain D and resid 1:100)D1 - 100
8X-RAY DIFFRACTION8(chain D and resid 101:264)D101 - 264

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