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

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Basic information

Entry
Database: PDB / ID: 6rbv
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-(3-azidopropyl)-8-bromanyl-purin-6-amine / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)31,5353
Polymers31,0451
Non-polymers4892
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)126,13812
Polymers124,1814
Non-polymers1,9578
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 area9780 Å2
ΔGint-53 kcal/mol
Surface area44050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.442, 76.726, 118.758
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Components on special symmetry positions
IDModelComponents
11A-436-

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-JYE / 9-(3-azidopropyl)-8-bromanyl-purin-6-amine


Mass: 297.115 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9BrN8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.31 % / Mosaicity: 1.43 °
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: ID29 / Wavelength: 0.979338 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 2.29→32.22 Å / Num. obs: 12936 / % possible obs: 98.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 31.05 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.062 / Rrim(I) all: 0.133 / Net I/σ(I): 7 / Num. measured all: 55622 / Scaling rejects: 104
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
2.29-2.374.50.479553912390.8930.2450.5412.698.5
8.87-32.2240.0989732430.9870.0520.11113.694

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
MOSFLMdata reduction
Aimless0.7.1data scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→32.22 Å / SU ML: 0.3119 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.5312
RfactorNum. reflection% reflection
Rfree0.2403 609 4.83 %
Rwork0.1834 --
obs0.186 12602 95.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.88 Å2
Refinement stepCycle: LAST / Resolution: 2.29→32.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2097 0 30 92 2219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00172222
X-RAY DIFFRACTIONf_angle_d0.49723012
X-RAY DIFFRACTIONf_chiral_restr0.0453323
X-RAY DIFFRACTIONf_plane_restr0.0029386
X-RAY DIFFRACTIONf_dihedral_angle_d17.3641317
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.520.30431590.22682929X-RAY DIFFRACTION95.1
2.52-2.880.24611560.21042981X-RAY DIFFRACTION96.49
2.88-3.630.22921460.18333007X-RAY DIFFRACTION95.63
3.63-31.520.22681480.16223076X-RAY DIFFRACTION94.38
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)
13.45567534732-0.848135509931-1.839323473912.165398757740.8864037782656.07716130571-0.109574508601-0.5273330973140.3132827938760.2056342494260.1170816186290.0559462541479-0.119357665348-0.1374647447660.01072654827360.2933490902290.04475730377480.01324091184530.455934450568-0.1051137017150.2974341477412.250400541624.125429467622.958321759
22.530999500660.2058543952430.403946996062.7595368970.5260186626692.877131465710.08296931544270.1416915621310.276961056766-0.0869547646284-0.0402223009010.251597348756-0.210388541836-0.4575880507410.007221684306210.1852068312510.02757621873170.04030188658960.272075485910.04205050364580.21589593760518.012445254815.5825130182-1.81079517822
33.16192003167-0.2882317410940.9646683126161.461923272280.07335880642114.133255419930.05602853037120.04422382783250.0534218685093-0.0812315088998-0.008413979280650.1494557818780.0585276060754-0.217395456106-0.0402528590590.1780722302940.01062619514710.0396602572540.1862549593370.03790877548290.22430702313619.492344828914.44143379540.477973225408
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 91 )
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 184 )
3X-RAY DIFFRACTION3chain 'A' and (resid 185 through 264 )

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