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

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Basic information

Entry
Database: PDB / ID: 6rgb
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-K38 / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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

Downloads & links

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Assembly

Deposited unit
A: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8073
Polymers31,0451
Non-polymers7622
Water1,65792
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)127,22812
Polymers124,1814
Non-polymers3,0478
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)62.790, 75.620, 118.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22

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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-K38 / (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-ynylamino]methyl]oxolane-3,4-diol


Mass: 569.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27N11O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 45.53 % / Mosaicity: 0.92 °
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: Jun 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.25→37.81 Å / Num. obs: 13690 / % possible obs: 99.5 % / Redundancy: 5.4 % / Biso Wilson estimate: 30.39 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.034 / Rrim(I) all: 0.082 / Net I/σ(I): 16.4 / Num. measured all: 74351 / Scaling rejects: 233
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
2.25-2.324.90.48598412120.790.2540.5483.597.9
8.98-37.814.60.02911302450.9990.0140.03341.197.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
MOSFLMdata reduction
Aimless0.7.2data scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→37.39 Å / SU ML: 0.2467 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.142 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2306 694 5.09 %
Rwork0.2062 12932 -
obs0.2075 13626 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.71 Å2
Refinement stepCycle: LAST / Resolution: 2.25→37.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2075 0 54 92 2221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00832226
X-RAY DIFFRACTIONf_angle_d0.6893022
X-RAY DIFFRACTIONf_chiral_restr0.0551326
X-RAY DIFFRACTIONf_plane_restr0.0034383
X-RAY DIFFRACTIONf_dihedral_angle_d20.20731311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.420.32891330.27752472X-RAY DIFFRACTION96.41
2.42-2.660.2671330.23682577X-RAY DIFFRACTION99.34
2.66-3.050.23171450.23092566X-RAY DIFFRACTION99.45
3.05-3.840.20611320.19692621X-RAY DIFFRACTION99.71
3.84-37.40.21671510.17792696X-RAY DIFFRACTION99.13
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)
13.339966236230.0328871141332-1.245357486530.9638701981980.3369585530455.51025794755-0.0465661703928-0.3508546970430.2057402734040.1461113753950.001583162106160.0800892521621-0.422530736306-0.218290785537-0.02169243919240.3824927754080.1205948884380.01545114415730.407683368197-0.1050754715070.27118115638410.120635406924.707764995822.1197048992
23.79441493299-0.00529631052913-1.604071644540.0751177535862-0.09087637933856.12575294563-0.340872671619-0.980371670670.5278994732310.2519450422630.626499807244-0.4818008887730.3190686997930.9429517649640.02616554289880.4313808364180.1702598939430.02917439502860.699398606707-0.1238220351570.44361017052520.550793985221.117209744726.3268912812
32.187017823350.358251785264-0.4026300720461.738373840960.293202789133.326683876080.01161865672070.03140097801630.220886046488-0.0268180649952-0.1092231986960.315232187064-0.400446178687-0.5896406644020.1629897184670.2045573053450.08708201933690.002974460511680.3268651485710.02140267497750.30055168241114.704312794918.2407359353-1.08660006621
41.816970223160.0947135552730.3419632026481.604319861420.9991726303983.625247538930.002692419250240.07243888105110.0280588855725-0.1405431175123.17819052678E-50.128431558279-0.185405493116-0.1030612792760.0275493846850.1531809716280.02620178330130.004386655733560.146997537232-0.000773165234360.18377153586923.255331872911.8383081274-1.98931347112
51.65556826655-0.214873615525-0.3778956219021.816155729140.3749954019583.123656694420.07667555997190.1115384363350.0771604597387-0.00293180070056-0.1488774581580.28513571006-0.0718082217493-0.4110676406650.08238597751520.2114112178210.045802059433-0.005474955581470.2533583141660.01715456294860.27533040880517.311537252514.4931228822-2.89682967908
65.008915568180.705021859365-0.3756743922144.786034100142.002551866525.335048117420.0305002481505-0.988441819182-0.09958956255170.9091188410270.276377314847-0.1286732916120.4092319559640.122228469458-0.02900280408160.2716506848920.03169111680790.04495550261070.327086925642-0.02875433994880.21890030893131.503089192512.825836861217.5076182638
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 68 )
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 92 )
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 141 )
4X-RAY DIFFRACTION4chain 'A' and (resid 142 through 184 )
5X-RAY DIFFRACTION5chain 'A' and (resid 185 through 252 )
6X-RAY DIFFRACTION6chain 'A' and (resid 253 through 264 )

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