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- PDB-2i29: Crystal structure of NAD kinase 1 from Listeria monocytogenes -

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Basic information

Entry
Database: PDB / ID: 2i29
TitleCrystal structure of NAD kinase 1 from Listeria monocytogenes
ComponentsProbable inorganic polyphosphate/ATP-NAD kinase 1
KeywordsTRANSFERASE / NAD-bound NAD kinase in orthorhombic form
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
CITRIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPoncet-Montange, G. / Assairi, L. / Arold, S. / Pochet, S. / Labesse, 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 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Jun 24, 2020Group: Advisory / Database references / Derived calculations
Category: database_PDB_caveat / pdbx_struct_assembly ...database_PDB_caveat / pdbx_struct_assembly / pdbx_struct_assembly_gen / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,9013
Polymers31,0451
Non-polymers8562
Water1,38777
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)127,60312
Polymers124,1814
Non-polymers3,4228
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 area12670 Å2
ΔGint-70 kcal/mol
Surface area37880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.503, 73.538, 118.745
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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 EGD-e (bacteria)
Species: Listeria monocytogenes / Strain: EGD-E / Gene: ppnK1 / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y8D7, NAD+ kinase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.28 Å3/Da / Density % sol: 45.94 %
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→37.14 Å / Num. all: 16111 / Num. obs: 15633 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 17.2

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I1W

2i1w


Resolution: 2.1→34.86 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.917 / SU B: 11.179 / SU ML: 0.148 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.254 478 3 %RANDOM
Rwork0.205 ---
all0.206 16111 --
obs0.206 15633 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.011 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2--3.79 Å20 Å2
3----4.47 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 57 77 2110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212122
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9642887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3425256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08223.43896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.74115329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9561511
X-RAY DIFFRACTIONr_chiral_restr0.1630.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021617
X-RAY DIFFRACTIONr_nbd_refined0.2120.2889
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21383
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2990.2115
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2960.210
X-RAY DIFFRACTIONr_mcbond_it0.4551.51320
X-RAY DIFFRACTIONr_mcangle_it0.70722041
X-RAY DIFFRACTIONr_scbond_it1.0553930
X-RAY DIFFRACTIONr_scangle_it1.2444.5844
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 31 -
Rwork0.283 981 -
obs-1012 85.19 %
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)
13.0171-0.3055-1.59850.67461.61876.779-0.0522-0.17310.13790.01560.05780.0787-0.1871-0.2483-0.00560.01840.04650.04340.0561-0.0664-0.044810.853623.213321.926
21.88040.87370.16330.45560.51593.9143-0.0498-0.57120.34610.08450.2446-0.196-0.2550.25-0.19490.1640.03510.07330.1199-0.11110.059121.858525.616625.8639
33.53433.9782-2.417413.7832.68397.14810.1645-0.54910.14940.6995-0.0788-0.0115-0.0402-0.0301-0.0857-0.0923-0.0169-0.0194-0.0357-0.0482-0.171131.090813.700116.6672
41.469-0.14630.09571.89020.46992.89950.09260.04840.1337-0.0799-0.13180.2879-0.1911-0.32110.0391-0.12710.05180.0064-0.12020.0104-0.103717.532713.3537-4.2049
50.03160.64050.059912.98671.21350.1134-0.0127-2.0793-0.40610.97070.05260.60920.1179-1.4235-0.040.04630.01140.08360.2020.0380.055417.13138.729611.1169
6148.714743.031933.129154.441120.43738.2094-1.47293.98241.66780.43823.4690.56621.1516-6.127-1.99610.10350.04890.01890.0434-0.07590.008730.860224.919313.594
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 DIFFRACTION6A274

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