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- PDB-2i2d: Crystal structure of LmNADK1 -

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Basic information

Entry
Database: PDB / ID: 2i2d
TitleCrystal structure of LmNADK1
ComponentsProbable inorganic polyphosphate/ATP-NAD kinase 1
KeywordsTRANSFERASE / Crystal structure of LmNADK1 bound to a NAD analog
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
Chem-A2D / CITRIC ACID / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsPoncet-Montange, G. / 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 / 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 1.3Aug 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_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)31,9143
Polymers31,0451
Non-polymers8692
Water1,06359
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)127,65512
Polymers124,1814
Non-polymers3,4748
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)62.481, 75.851, 118.350
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-302-

HOH

21A-314-

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) / Strain: Bacteria / Gene: ppnK1 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y8D7, NAD+ kinase
#2: Chemical ChemComp-A2D / BIS{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL} DIHYDROGEN DIPHOSPHATE / BIS(ADENOSINE)-5'-DIPHOSPHATE


Mass: 676.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26N10O13P2
#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.: 59 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
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: ID23-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.22→37.9 Å / Num. all: 13780 / Num. obs: 13383 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 22.9
Reflection shellResolution: 2.22→2.34 Å / Redundancy: 4 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 3.5 / % possible all: 81.2

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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 2i2b

2i2b


Resolution: 2.22→37.93 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.595 / SU ML: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.306 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 405 2.9 %RANDOM
Rwork0.207 ---
all0.208 13780 --
obs0.208 13383 96.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.883 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2--1.85 Å20 Å2
3----2.54 Å2
Refinement stepCycle: LAST / Resolution: 2.22→37.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1979 0 58 59 2096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212101
X-RAY DIFFRACTIONr_bond_other_d0.0040.025
X-RAY DIFFRACTIONr_angle_refined_deg2.2571.9662854
X-RAY DIFFRACTIONr_angle_other_deg0.958311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3475254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03623.54893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10315324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3711510
X-RAY DIFFRACTIONr_chiral_restr0.3390.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021595
X-RAY DIFFRACTIONr_nbd_refined0.2180.2892
X-RAY DIFFRACTIONr_nbd_other0.0630.26
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21373
X-RAY DIFFRACTIONr_nbtor_other0.1160.25
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.292
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3350.25
X-RAY DIFFRACTIONr_mcbond_it0.4721.51306
X-RAY DIFFRACTIONr_mcangle_it0.77822026
X-RAY DIFFRACTIONr_scbond_it1.1163929
X-RAY DIFFRACTIONr_scangle_it1.5024.5827
LS refinement shellResolution: 2.22→2.277 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 29 -
Rwork0.231 760 -
obs-789 75.79 %
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)
13.0554-0.2742-1.46671.23931.02915.4419-0.1057-0.06120.03330.0520.03160.1618-0.0978-0.24030.07410.00560.04720.03150.0009-0.0569-0.062410.713823.875121.5719
22.23420.4488-1.71260.38880.71785.08790.0017-0.75590.28710.07930.2158-0.1461-0.21090.0805-0.21760.13140.03830.01190.2044-0.11210.096921.608826.322725.7091
31.07633.821-1.958215.3909-3.329710.74290.0291-0.329-0.08460.91460.0177-0.3357-0.14280.075-0.0468-0.0921-0.00370.0247-0.0697-0.0284-0.153931.402613.543216.8324
41.5218-0.2951-0.10231.98780.20982.54760.0380.11080.0637-0.1294-0.05460.35330.0113-0.3540.0166-0.1050.02320.0014-0.07890.0144-0.12617.480613.3998-4.3418
547.043-0.368631.629592.869812.251222.9484-0.4663-1.1696-2.59040.56611.42881.37550.4782-2.1383-0.96240.1742-0.0380.11390.17740.0554-0.031718.37699.830413.3409
6267.979-165.0771-21.1956164.496977.609768.0229-0.8604-2.89083.0349-6.3-0.6377-1.661-4.40993.63531.49810.2683-0.21280.00990.19890.0478-0.002829.839924.509914.3665
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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