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- PDB-3v7w: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -

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Basic information

Entry
Database: PDB / ID: 3v7w
TitleCrystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 5'-azido-5'-deoxyadenosine
ComponentsProbable inorganic polyphosphate/ATP-NAD kinase 1
KeywordsTRANSFERASE / ligand-screening by crystallography / Two-domain kinase / Inorganic polyphosphate/ATP-NAD kinase 1
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 / 5'-azido-5'-deoxyadenosine / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Isomorphous replacement / Resolution: 2.0102 Å
AuthorsGelin, M. / Poncet-Montange, G. / Assairi, L. / Morellato, L. / Huteau, V. / Dugu, L. / Dussurget, O. / Pochet, S. / Labesse, G.
CitationJournal: Structure / Year: 2012
Title: Screening and In Situ Synthesis Using Crystals of a NAD Kinase Lead to a Potent Antistaphylococcal Compound.
Authors: Gelin, M. / Poncet-Montange, G. / Assairi, L. / Morellato, L. / Huteau, V. / Dugue, L. / Dussurget, O. / Pochet, S. / Labesse, G.
History
DepositionDec 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references
Revision 1.2Jun 27, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 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
Revision 2.0May 15, 2024Group: Data collection / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / entity
Item: _chem_comp.formula / _chem_comp.formula_weight / _entity.formula_weight

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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)31,9145
Polymers31,0451
Non-polymers8694
Water1,60389
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)127,65620
Polymers124,1814
Non-polymers3,47516
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 area10730 Å2
ΔGint-35 kcal/mol
Surface area37910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.912, 74.026, 118.419
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 / Poly(P)/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, lmo0968 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y8D7, NAD+ kinase
#2: Chemical ChemComp-ZAS / 5'-azido-5'-deoxyadenosine


Mass: 292.254 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N8O3
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#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.: 89 / 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: 2.22 Å3/Da / Density % sol: 44.61 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 30 mM sodium bromide, 220 mM potassium citrate, pH 4.8-5.1, glycerol 6%, 15-16% w/v polyethylene glycol 400, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 12, 2007
RadiationMonochromator: Asymmetric Laue 001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.01→62.75 Å / Num. obs: 18364 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 %
Reflection shellResolution: 2.01→2.12 Å / Redundancy: 5.6 % / % possible all: 94

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: Isomorphous replacement / Resolution: 2.0102→37.258 Å / SU ML: 0.26 / σ(F): 1.06 / Phase error: 21.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2039 556 3.02 %
Rwork0.1865 --
obs0.187 18364 96.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.879 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.3822 Å20 Å2-0 Å2
2--11.8483 Å20 Å2
3----12.2304 Å2
Refinement stepCycle: LAST / Resolution: 2.0102→37.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2043 0 61 89 2193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062196
X-RAY DIFFRACTIONf_angle_d0.842979
X-RAY DIFFRACTIONf_dihedral_angle_d14.928793
X-RAY DIFFRACTIONf_chiral_restr0.056327
X-RAY DIFFRACTIONf_plane_restr0.002377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0102-2.11620.28971570.29214560X-RAY DIFFRACTION92
2.1162-2.24870.29551610.25314767X-RAY DIFFRACTION97
2.2487-2.42230.26841510.22964758X-RAY DIFFRACTION97
2.4223-2.6660.23691480.19514810X-RAY DIFFRACTION98
2.666-3.05170.22731480.18494806X-RAY DIFFRACTION97
3.0517-3.84420.1871280.15824867X-RAY DIFFRACTION98
3.8442-37.2640.13891490.1594846X-RAY DIFFRACTION98
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)
10.7339-0.3589-0.50940.6050.49870.4917-0.0219-0.2792-0.01670.04450.05040.0793-0.0568-0.1749-0.00270.37920.08230.04890.4074-0.10430.249913.456923.765222.8304
20.5594-0.175-0.15630.85580.23161.97460.0692-0.00390.05420.0209-0.09990.1421-0.0411-0.27090.02760.04330.05320.00970.0883-0.00590.078519.267713.3512-1.5927
30.4729-0.3631-0.31570.21130.22310.17950.02680.0175-0.0903-0.0481-0.08990.1421-0.1702-0.1830.05360.16410.0280.00170.2202-0.01130.171518.383113.88113.0063
40.20680.3608-0.24191.1419-0.06940.95320.0534-0.02330.0088-0.00890.0469-0.0493-0.14650.0266-0.08030.53030.1092-0.08270.3958-0.20090.404530.063724.819315.1278
51.4383-0.9576-2.08194.04582.83263.6265-0.169-0.0804-0.09980.6798-0.02340.20750.17180.02560.15380.5236-0.05850.12760.2638-0.07620.260718.09448.562811.0681
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:100)
2X-RAY DIFFRACTION2(chain A and resid 101:264)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 401:489)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 303:303)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 301:302)

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