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- PDB-6rc2: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -

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Basic information

Entry
Database: PDB / ID: 6rc2
TitleCrystal structure of NAD kinase 1 from Listeria monocytogenes in complexe with an adenine 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
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 / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / 8-methyl-9-pent-4-ynyl-purin-6-amine / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.048 Å
AuthorsGelin, M. / Labesse, G.
CitationJournal: Acs Infect Dis. / Year: 2020
Title: From Substrate to Fragments to Inhibitor ActiveIn VivoagainstStaphylococcus aureus.
Authors: Gelin, M. / Paoletti, J. / Nahori, M.A. / Huteau, V. / Leseigneur, C. / Jouvion, G. / Dugue, L. / Clement, D. / Pons, J.L. / Assairi, L. / Pochet, S. / Labesse, G. / Dussurget, O.
History
DepositionApr 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4533
Polymers31,0451
Non-polymers4072
Water1,17165
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)125,81112
Polymers124,1814
Non-polymers1,6308
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
Unit cell
Length a, b, c (Å)62.422, 76.438, 118.130
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-424-

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 (E. coli) / 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-JY2 / 8-methyl-9-pent-4-ynyl-purin-6-amine


Mass: 215.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13N5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 291.15 K / Method: evaporation / pH: 5
Details: 30 mM NaBr, 220 mM Kcitrate, glycerol 6%, 15-16% w/v PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.047→64.167 Å / Num. obs: 18022 / % possible obs: 99 % / Redundancy: 4.5 % / Biso Wilson estimate: 40.34 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.02 / Rrim(I) all: 0.045 / Net I/σ(I): 18.4 / Num. measured all: 81554
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
2.047-2.0834.10.59537409030.8750.3280.6842.199.7
5.556-64.1674.20.019409697310.010.0215497.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.048→64.167 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.68
RfactorNum. reflection% reflection
Rfree0.2268 930 5.18 %
Rwork0.2039 --
obs0.2051 17960 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.79 Å2 / Biso mean: 51.7915 Å2 / Biso min: 28.34 Å2
Refinement stepCycle: final / Resolution: 2.048→64.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 29 65 2172
Biso mean--69.12 50.37 -
Num. residues----261
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0475-2.15550.32651180.29282418253699
2.1555-2.29050.29461410.2842378251999
2.2905-2.46740.28531210.24092435255699
2.4674-2.71570.2531390.22472387252698
2.7157-3.10870.29641310.23632410254198
3.1087-3.91650.19281380.18552465260399
3.9165-64.20630.1951420.17662537267998
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)
12.9341-0.2355-0.36390.69930.21884.4725-0.1058-0.43540.31670.1413-0.02680.138-0.3719-0.56780.11580.47080.08580.04270.5376-0.11410.42348.927124.552823.6963
23.3526-1.68490.01323.6848-0.22023.5028-0.173-0.2978-0.05620.16160.21830.1348-0.0261-0.1842-0.01830.47520.05020.07870.5053-0.05350.415816.836221.569818.0039
32.2468-0.3061-0.13461.90750.62142.50830.06680.01680.2459-0.0174-0.01020.1956-0.2341-0.2567-0.02560.25760.01650.03120.29250.0270.292318.653216.66481.8832
43.28571.67110.4474.93370.3372.2803-0.13710.5891-0.3168-0.97890.29930.03280.4080.0233-0.07010.63480.0378-0.00540.54570.02090.352225.67270.9752-13.411
53.88520.4571-0.21242.6006-0.38843.74130.05720.34590.1685-0.1127-0.0380.53850.1082-0.8147-0.00840.29960.0584-0.00230.43-0.00690.400712.238513.2732-6.4753
62.683-0.9875-0.11142.77940.95981.739-0.0706-0.35040.48170.19590.0435-0.01-0.4427-0.0477-0.0570.3542-0.01580.0780.2608-0.0470.340423.860619.624310.6474
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 55 )A1 - 55
2X-RAY DIFFRACTION2chain 'A' and (resid 56 through 79 )A56 - 79
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 184 )A80 - 184
4X-RAY DIFFRACTION4chain 'A' and (resid 185 through 198 )A185 - 198
5X-RAY DIFFRACTION5chain 'A' and (resid 199 through 230 )A199 - 230
6X-RAY DIFFRACTION6chain 'A' and (resid 231 through 264 )A231 - 264

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