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- PDB-3v7y: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -

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Basic information

Entry
Database: PDB / ID: 3v7y
TitleCrystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 5'-N-Propargylamino-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 / NADP biosynthetic process / NAD+ kinase activity / NAD metabolic process / NAD binding / phosphorylation / 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 / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / NAD kinase/diacylglycerol kinase-like domain superfamily / 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 / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / NAD kinase/diacylglycerol kinase-like domain superfamily / Tumour Suppressor Smad4 / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5'-deoxy-5'-(prop-2-yn-1-ylamino)adenosine / CITRIC ACID / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Isomorphous replacement / Resolution: 1.97 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 1.4Jun 24, 2020Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)31,8464
Polymers31,0451
Non-polymers8013
Water1,856103
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)127,38416
Polymers124,1814
Non-polymers3,20312
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)62.812, 75.675, 118.619
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-456-

HOH

21A-471-

HOH

31A-489-

HOH

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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-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-A3N / 5'-deoxy-5'-(prop-2-yn-1-ylamino)adenosine


Mass: 304.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H16N6O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.27 Å3/Da / Density % sol: 45.82 %
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: ID29 / Wavelength: 0.979338 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2011
RadiationMonochromator: Asymmetric Laue 001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 1.97→48.34 Å / Num. obs: 20293 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 %
Reflection shellResolution: 1.97→2.08 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: Isomorphous replacement / Resolution: 1.97→48.332 Å / SU ML: 0.32 / σ(F): 1.06 / Phase error: 26.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2292 603 2.96 %
Rwork0.1934 --
obs0.1944 20293 94.83 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.342 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6236 Å20 Å2-0 Å2
2--8.6491 Å20 Å2
3----10.2727 Å2
Refinement stepCycle: LAST / Resolution: 1.97→48.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 57 103 2214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092218
X-RAY DIFFRACTIONf_angle_d0.9253010
X-RAY DIFFRACTIONf_dihedral_angle_d15.949813
X-RAY DIFFRACTIONf_chiral_restr0.064327
X-RAY DIFFRACTIONf_plane_restr0.003378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.05970.41091280.3114463X-RAY DIFFRACTION96
2.0597-2.16830.28631570.26434459X-RAY DIFFRACTION95
2.1683-2.30410.35731330.29334181X-RAY DIFFRACTION89
2.3041-2.4820.33641370.22614490X-RAY DIFFRACTION96
2.482-2.73180.24041290.19764516X-RAY DIFFRACTION96
2.7318-3.1270.23611570.19194473X-RAY DIFFRACTION96
3.127-3.93950.19651110.16114477X-RAY DIFFRACTION95
3.9395-48.34660.1781330.17274486X-RAY DIFFRACTION95
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)
11.4085-0.4457-0.66060.56210.26810.4436-0.0951-0.45390.06840.01990.1180.0005-0.06710.0437-0.00630.38930.08570.04390.4517-0.10480.278813.39624.231822.589
20.7163-0.1503-0.00511.18330.33281.94290.06630.00930.0678-0.0285-0.06180.1666-0.057-0.2609-0.01010.19760.03290.01270.25550.00850.225119.007313.6376-2.0038
30.4669-0.3241-0.22020.37920.35890.36530.03690.07170.0311-0.0486-0.01160.1191-0.0763-0.2257-0.0280.31650.02270.00910.31050.00380.291217.920116.50733.6813
43.53274.71973.563129.53576.99340.105-0.22530.2532-0.0206-0.45010.6086-0.0228-0.22010.35020.5160.0586-0.02370.8646-0.52150.652329.715724.682615.1991
50.51260.3385-0.85250.2387-0.69622.5995-0.0405-0.7149-0.07520.1274-0.11020.0938-0.1571-0.16910.1170.7677-0.06980.21740.6626-0.09840.524117.68238.719411.092
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:100)
2X-RAY DIFFRACTION2(chain A and resid 101:263)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 401:503)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 301:301)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 302:303)

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