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

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Basic information

Entry
Database: PDB / ID: 6rbq
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 / ~{S}-[4-(6-aminopurin-9-yl)butyl] ethanethioate / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.236 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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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)31,5033
Polymers31,0451
Non-polymers4572
Water77543
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)126,01112
Polymers124,1814
Non-polymers1,8308
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 area9510 Å2
ΔGint-51 kcal/mol
Surface area42250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.992, 76.354, 118.110
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-418-

HOH

21A-439-

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-JYQ / ~{S}-[4-(6-aminopurin-9-yl)butyl] ethanethioate


Mass: 265.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.25 Å3/Da / Density % sol: 45.36 %
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: ID30B / Wavelength: 0.98792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98792 Å / Relative weight: 1
ReflectionResolution: 2.24→54.96 Å / Num. obs: 13372 / % possible obs: 96.1 % / Redundancy: 4.4 % / Biso Wilson estimate: 38.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.038 / Rrim(I) all: 0.083 / Net I/σ(I): 10.9 / Num. measured all: 58492
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
2.24-2.2794.30.53728446540.8160.2850.6122.595.8
6.078-54.963.90.0428507230.9980.0210.04628.393.9

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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: 2.236→54.891 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.24
RfactorNum. reflection% reflection
Rfree0.2646 645 4.84 %
Rwork0.2311 --
obs0.2327 13333 95.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 131.98 Å2 / Biso mean: 52.6268 Å2 / Biso min: 23.87 Å2
Refinement stepCycle: final / Resolution: 2.236→54.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2052 0 31 43 2126
Biso mean--52.05 43.58 -
Num. residues----261
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.236-2.40860.29751240.32142443256794
2.4086-2.6510.34721350.28472515265096
2.651-3.03460.32331230.27512506262996
3.0346-3.82310.28281340.22462575270997
3.8231-54.90710.21561290.19442649277896
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)
14.5244-0.7814-0.344.7940.90484.28110.2128-0.66860.04530.2233-0.35570.0253-0.31060.0880.22560.41150.06780.02250.9069-0.05980.38898.493722.861228.6116
22.5901-0.0089-1.3282.0254-0.07384.13190.0008-0.55310.33560.17920.05090.1005-0.1127-0.2498-0.04430.39370.05710.03560.7687-0.12250.421713.455225.063920.5917
34.31790.5494-0.0753.9664-0.37212.7426-0.18810.18811.03110.115-0.14980.6338-0.51940.13280.30550.36510.07860.04340.6625-0.03270.446513.731724.49433.2299
42.24040.4527-0.33682.46440.87724.17360.06450.31740.10980.2715-0.01420.0422-0.0132-0.2108-0.07310.24890.01340.0250.37610.03590.290620.454711.41-3.7635
54.1253-1.9419-0.46870.92010.2870.97890.39550.596-0.8181-0.6603-0.17050.23850.26-0.5170.16340.6671-0.0541-0.09860.83310.01070.344724.96771.3478-12.4037
64.42190.024-0.11171.8472-0.52932.5869-0.05420.3159-0.1436-0.0940.10290.35080.2901-0.3249-0.0840.31950.0505-0.00520.5581-0.01220.329712.006113.3135-6.4687
73.7677-0.9554-0.63123.05150.82090.6385-0.022-0.26790.27030.2559-0.03140.021-0.10710.52250.04210.34-0.05370.09630.4651-0.04480.36923.632919.724810.5581
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 26 )A1 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 92 )A27 - 92
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 120 )A93 - 120
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 184 )A121 - 184
5X-RAY DIFFRACTION5chain 'A' and (resid 185 through 198 )A185 - 198
6X-RAY DIFFRACTION6chain 'A' and (resid 199 through 230 )A199 - 230
7X-RAY DIFFRACTION7chain 'A' and (resid 231 through 264 )A231 - 264

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