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- PDB-2i2a: Crystal structure of LmNADK1 from Listeria monocytogenes -

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Basic information

Entry
Database: PDB / ID: 2i2a
TitleCrystal structure of LmNADK1 from Listeria monocytogenes
ComponentsProbable inorganic polyphosphate/ATP-NAD kinase 1
KeywordsTRANSFERASE / NADP bound crystal structure of LmNADK1
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 1 / 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 ...Probable inorganic polyphosphate/atp-NAD kinase; domain 1 / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsLabesse, G.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: NAD kinases use substrate-assisted catalysis for specific recognition of NAD.
Authors: Poncet-Montange, G. / Assairi, L. / Arold, S. / Pochet, S. / Labesse, G.
History
DepositionAug 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.2Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable inorganic polyphosphate/ATP-NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8813
Polymers31,0451
Non-polymers8352
Water2,216123
1
A: Probable inorganic polyphosphate/ATP-NAD kinase 1
hetero molecules

A: Probable inorganic polyphosphate/ATP-NAD kinase 1
hetero molecules

A: Probable inorganic polyphosphate/ATP-NAD kinase 1
hetero molecules

A: Probable inorganic polyphosphate/ATP-NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,52312
Polymers124,1814
Non-polymers3,3428
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 area13020 Å2
ΔGint-49 kcal/mol
Surface area40100 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)61.902, 77.429, 117.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-336-

HOH

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Components

#1: Protein Probable inorganic polyphosphate/ATP-NAD kinase 1 / PolyP / /ATP NAD kinase 1


Mass: 31045.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: ppnK1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y8D7, NAD+ kinase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.4
Details: 0.3 M potassium chloride, 50 mM tri-sodium citrate dihydrate, 15-20% w/v polyethylene glycol 400, pH 5.4, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→37.37 Å / Num. all: 15714 / Num. obs: 15714 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.1
Reflection shellResolution: 2.1→2.21 Å / % possible all: 91.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→37.37 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 12.447 / SU ML: 0.165 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 477 2.9 %RANDOM
Rwork0.199 ---
all0.201 16191 --
obs0.201 15714 95.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.292 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--2.33 Å20 Å2
3----2.15 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 54 123 2236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212177
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9672957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5765265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68923.60897
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.99315346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.051511
X-RAY DIFFRACTIONr_chiral_restr0.140.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021643
X-RAY DIFFRACTIONr_nbd_refined0.2130.2933
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21431
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2770.2144
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.214
X-RAY DIFFRACTIONr_mcbond_it0.4631.51357
X-RAY DIFFRACTIONr_mcangle_it0.76722105
X-RAY DIFFRACTIONr_scbond_it1.1113943
X-RAY DIFFRACTIONr_scangle_it1.64.5851
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 41 -
Rwork0.251 1183 -
obs-1224 97.92 %
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)
13.2378-0.5895-1.12670.9081.88896.1532-0.0965-0.29780.04240.02640.06570.0026-0.1944-0.2450.0309-0.04990.03490.03-0.031-0.0472-0.049810.69623.936921.6522
23.00580.3257-1.47210.0353-0.15950.72090.0721-0.68930.47120.08720.221-0.37-0.41770.37-0.29310.26190.06780.04560.2432-0.15310.168321.422227.130725.2361
37.69013.8542-2.430111.5189-1.00117.3265-0.121-0.23830.09941.09160.1226-0.0627-0.2533-0.4743-0.0016-0.08690.0027-0.013-0.0233-0.0603-0.173630.813413.456716.8111
41.8079-0.15070.02551.88020.27182.30370.06010.17670.1901-0.1291-0.08450.2451-0.0659-0.21150.0244-0.13250.0350.0058-0.09750.0264-0.127316.860113.4824-4.6474
51.0205-2.92841.145911.0071-1.78442.15490.2743-1.3125-0.84710.5872-0.19920.46020.5134-1.9609-0.07520.0964-0.08260.09970.06960.00210.05316.35798.965911.2852
6132.9807102.869680.2875283.682537.147651.52623.39961.58782.81511.4423-1.7664-2.07550.01523.525-1.63320.0128-0.13220.07080.02660.0215-0.002631.84524.879713.5849
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 76
2X-RAY DIFFRACTION2A77 - 97
3X-RAY DIFFRACTION2A245 - 251
4X-RAY DIFFRACTION3A252 - 263
5X-RAY DIFFRACTION4A98 - 244
6X-RAY DIFFRACTION5A273
7X-RAY DIFFRACTION6A301

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