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

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Basic information

Entry
Database: PDB / ID: 6rgc
TitleCrystal structure of NAD kinase 1 from Listeria monocytogenes in complexe with an 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 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 / Chem-K3H / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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 16, 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

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Assembly

Deposited unit
A: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8213
Polymers31,0451
Non-polymers7762
Water1,856103
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)127,28412
Polymers124,1814
Non-polymers3,1038
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 area10780 Å2
ΔGint-44 kcal/mol
Surface area39840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.198, 74.809, 118.699
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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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-K3H / (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[3-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]prop-2-ynyl-methyl-amino]methyl]oxolane-3,4-diol


Mass: 583.557 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H29N11O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.26 Å3/Da / Density % sol: 45.56 % / Mosaicity: 1.21 °
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: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.19→63.29 Å / Num. obs: 14784 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 34.34 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.047 / Rrim(I) all: 0.089 / Net I/σ(I): 12.1 / Num. measured all: 49611 / Scaling rejects: 11
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
2.19-2.262.60.53324012550.6990.3620.6461.798
9.03-63.292.80.0296832430.9950.0210.03637.497.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimless0.7.2data scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→63.289 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25
RfactorNum. reflection% reflection
Rfree0.2265 724 4.9 %
Rwork0.1932 --
obs0.1948 14775 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.67 Å2 / Biso mean: 43.4332 Å2 / Biso min: 18.3 Å2
Refinement stepCycle: final / Resolution: 2.19→63.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 55 103 2227
Biso mean--36.48 45.25 -
Num. residues----259
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 (%)
2.1901-2.35920.35121440.28322723286799
2.3592-2.59660.28831480.238727812929100
2.5966-2.97230.24531330.221728102943100
2.9723-3.74480.21331540.181428132967100
3.7448-63.31490.19131450.16232924306999
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)
12.1303-0.3855-0.46470.68380.90963.8029-0.1888-0.21270.03610.16220.00780.2569-0.291-0.32410.16150.4770.08310.02440.5606-0.12050.39689.380824.000324.018
23.8574-0.87540.33643.0892-0.23055.0931-0.5578-0.168-0.05940.34540.2528-0.2741-0.0009-0.03880.14450.42630.08530.04790.415-0.09660.363616.784821.385718.1771
31.6417-0.4798-1.21251.37391.04823.71870.0896-0.00830.18240.0078-0.00870.1486-0.1467-0.3844-0.01790.20560.0389-0.00060.29410.01870.288517.868416.71552.6541
41.2464-0.3658-0.06071.81010.00272.82570.06890.00350.1487-0.0044-0.11710.2783-0.1509-0.28110.08370.25140.03460.00570.27450.00180.288321.012714.23580.3204
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 166 )A80 - 166
4X-RAY DIFFRACTION4chain 'A' and (resid 167 through 264 )A167 - 264

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