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- PDB-6rc1: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -

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Basic information

Entry
Database: PDB / ID: 6rc1
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 / 9-ethyl-8-methyl-purin-6-amine / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 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)31,4153
Polymers31,0451
Non-polymers3692
Water64936
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)125,65812
Polymers124,1814
Non-polymers1,4778
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)62.614, 75.775, 118.658
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-406-

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-JY8 / 9-ethyl-8-methyl-purin-6-amine


Mass: 177.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H11N5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 45.74 % / Mosaicity: 1.59 °
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: ID23-1 / Wavelength: 1.0017 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0017 Å / Relative weight: 1
ReflectionResolution: 2.54→63.86 Å / Num. obs: 9658 / % possible obs: 100 % / Redundancy: 8.3 % / Biso Wilson estimate: 44.52 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.061 / Rrim(I) all: 0.176 / Net I/σ(I): 10 / Num. measured all: 80201 / Scaling rejects: 44
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
2.54-2.658.51.375998711730.8570.4911.4612.1100
8.8-63.867.40.05619882700.9970.0230.06126.199.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimless0.7.1data scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.54→63.864 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.95
RfactorNum. reflection% reflection
Rfree0.2659 477 4.95 %
Rwork0.214 --
obs0.2165 9627 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.67 Å2 / Biso mean: 54.1383 Å2 / Biso min: 27.4 Å2
Refinement stepCycle: final / Resolution: 2.54→63.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 26 36 2120
Biso mean--68.05 46.82 -
Num. residues----259
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5402-2.90780.37271580.3052980313899
2.9078-3.66340.30131630.224130273190100
3.6634-63.88370.21571560.185731433299100
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)
12.76810.3647-1.24160.8428-0.17552.0913-0.0145-0.490.1670.1608-0.03450.0631-0.1436-0.1280.02110.56560.0740.01280.7601-0.16010.510211.530823.524122.0873
22.4791-0.3029-0.58861.30210.29822.71030.07770.05420.20010.06270.01620.0705-0.2003-0.28940.01140.29170.03520.0160.42960.00190.360918.98616.60682.4855
33.609-0.5387-0.72961.7912-0.01112.96520.17770.3231-0.0711-0.145-0.21710.51670.1625-0.61490.01270.41340.0788-0.0310.5178-0.02480.409815.511.3985-8.1684
43.487-1.0264-0.51342.6920.85883.2912-0.0859-0.70170.35160.59260.1411-0.0709-0.40210.1898-0.1430.5161-0.0640.06540.4868-0.14040.442526.889920.484115.8475
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 79 )A1 - 79
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 184 )A80 - 184
3X-RAY DIFFRACTION3chain 'A' and (resid 185 through 238 )A185 - 238
4X-RAY DIFFRACTION4chain 'A' and (resid 239 through 263 )A239 - 263

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