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- PDB-2i2f: Crystal structure of LmNADK1 -

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Basic information

Entry
Database: PDB / ID: 2i2f
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.2Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)31,8954
Polymers31,0441
Non-polymers8503
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)127,57916
Polymers124,1774
Non-polymers3,40212
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 area14660 Å2
ΔGint-95 kcal/mol
Surface area39300 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.428, 76.361, 119.202
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: 31044.295 Da / Num. of mol.: 1 / Mutation: D45N
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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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: 2.37 Å3/Da / Density % sol: 48.08 %
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: 0.934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→32.14 Å / Num. all: 22583 / Num. obs: 21902 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 20.9
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 4.1 / % possible all: 94

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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 2i29

2i29


Resolution: 1.9→32.14 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.706 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.243 681 3 %RANDOM
Rwork0.205 ---
all0.206 22583 --
obs0.206 21902 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.318 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2--1.41 Å20 Å2
3----2.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 55 59 2165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212191
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.9632975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.5025264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88523.2100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22515350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.041513
X-RAY DIFFRACTIONr_chiral_restr0.1130.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021654
X-RAY DIFFRACTIONr_nbd_refined0.1980.2918
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21433
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3030.295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.213
X-RAY DIFFRACTIONr_mcbond_it0.4241.51360
X-RAY DIFFRACTIONr_mcangle_it0.66322100
X-RAY DIFFRACTIONr_scbond_it0.8913964
X-RAY DIFFRACTIONr_scangle_it1.2274.5873
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 45 -
Rwork0.236 1442 -
obs-1487 89.74 %
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)
12.98950.1698-0.8090.53941.26556.0204-0.056-0.114-0.04650.0770.00570.0179-0.0312-0.14580.0503-0.00920.05230.0296-0.0169-0.0406-0.039410.948923.467122.1072
23.29570.833-1.37480.98041.51635.0854-0.1353-0.57060.28170.0580.1946-0.1273-0.16820.3245-0.05920.090.06160.0250.1284-0.07960.0221.639226.515725.7959
34.56831.95741.740312.66470.48445.74270.1535-0.37020.19140.4544-0.18540.13660.1711-0.31910.0319-0.0789-0.02490.0081-0.0282-0.0487-0.164331.118713.844616.6965
41.4245-0.154-0.2081.68590.29251.89490.02630.08480.0749-0.092-0.03190.2399-0.0665-0.26480.0056-0.1260.0201-0.0051-0.07640.0077-0.096817.325913.4018-4.4945
50.8427-3.1679-0.379511.9081.42640.17090.5054-0.7622-0.51111.9144-0.4784-0.00070.7165-0.3834-0.0270.15790.02010.0030.20040.02730.126617.04068.500111.0006
663.7448100.744835.0268230.531964.260591.77861.29510.85891.70830.45620.86770.8691-2.2033-1.4701-2.16280.02560.0590.01990.0455-0.07290.036831.693325.038413.4025
7341.48058.45881.8426228.9818-8.7711303.75280.10750.4959-1.1545-0.86331.3663-0.9932-0.1157-0.6408-1.47380.05430.0034-0.01280.0758-0.0060.068513.59788.573417.2022
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 DIFFRACTION5A274
7X-RAY DIFFRACTION6A301
8X-RAY DIFFRACTION7A273

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