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- PDB-3v8q: Crystal structure of NAD kinase 1 H223E mutant from Listeria mono... -

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Basic information

Entry
Database: PDB / ID: 3v8q
TitleCrystal structure of NAD kinase 1 H223E mutant from Listeria monocytogenes in complex with 5'-amino-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'-amino-5'-deoxyadenosine / CITRIC ACID / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Isomorphous replacement / Resolution: 2.37 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 23, 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: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / 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)31,5874
Polymers31,0361
Non-polymers5503
Water1,910106
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)126,34716
Polymers124,1454
Non-polymers2,20212
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)63.169, 75.060, 118.588
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-438-

HOH

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Components

#1: Protein Probable inorganic polyphosphate/ATP-NAD kinase 1 / Poly(P)/ATP NAD kinase 1


Mass: 31036.244 Da / Num. of mol.: 1 / Mutation: H233E
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-5N5 / 5'-amino-5'-deoxyadenosine


Mass: 266.257 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N6O3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


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


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.26 Å3/Da / Density % sol: 45.67 %
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: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 10, 2009
RadiationMonochromator: Asymmetric Laue 001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.29→48.45 Å / Num. obs: 11844 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 %
Reflection shellResolution: 2.29→2.41 Å / Redundancy: 4 % / % possible all: 100

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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: 2.37→48.331 Å / SU ML: 0.32 / σ(F): 1.36 / Phase error: 26.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2507 341 2.89 %
Rwork0.2057 --
obs0.207 11800 99.87 %
all-13024 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.457 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.57 Å20 Å2-0 Å2
2--14.1334 Å20 Å2
3----9.5635 Å2
Refinement stepCycle: LAST / Resolution: 2.37→48.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 38 106 2195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022164
X-RAY DIFFRACTIONf_angle_d0.5742925
X-RAY DIFFRACTIONf_dihedral_angle_d14.217798
X-RAY DIFFRACTIONf_chiral_restr0.04315
X-RAY DIFFRACTIONf_plane_restr0.002372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.98590.33391710.27435638X-RAY DIFFRACTION100
2.9859-48.3410.21841700.17965821X-RAY DIFFRACTION100
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)
11.1785-0.3985-0.70370.50070.39120.499-0.042-0.49930.0363-0.00940.1075-0.0138-0.08390.1491-0.05290.33030.06220.05430.3863-0.1050.194913.378824.208822.6462
20.4345-0.2560.05560.88550.45521.67970.04280.02940.092-0.0136-0.11880.04110.0061-0.21310.07510.08110.02830.00390.0995-0.01790.08919.24113.5607-1.8845
30.2428-0.33870.10040.4516-0.14750.25040.15340.0264-0.00180.0141-0.0998-0.10560.0335-0.0508-0.04550.1286-0.0025-0.00360.0463-0.00170.176617.475917.63646.2434
42-5.9613-9.8575.97265.48187.7838-0.042-0.17580.0837-0.01440.07220.064-0.05810.0288-0.02270.25680.03780.01660.7744-0.35720.688829.909924.588915.421
53.8436-3.7472-3.78573.85354.08394.5008-0.3794-0.2735-0.1959-0.057-0.18650.16520.2931-0.10640.49870.32340.16010.10310.4127-0.06270.207316.84937.64118.6862
626.41920.15282224.9820.98311.88453.0603-4.5940.5898-0.23345.1789-0.37240.8009-0.36330.12590.77270.0740.181720.829412.178212.4239
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 401:506
4X-RAY DIFFRACTION4(chain A and resid 303)
5X-RAY DIFFRACTION5(chain A and resid 301)
6X-RAY DIFFRACTION6(chain A and resid 302)

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