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- PDB-3v8n: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -

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Basic information

Entry
Database: PDB / ID: 3v8n
TitleCrystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 8-bromo-5'-amino-5'-deoxyadenosine, reacted with a citrate molecule in N site
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
Chem-5CI / 5'-amino-8-bromo-5'-deoxyadenosine / CITRIC ACID / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Isomorphous replacement / Resolution: 2.3801 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: 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)32,1024
Polymers31,0451
Non-polymers1,0573
Water1,45981
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)128,40716
Polymers124,1814
Non-polymers4,22612
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)63.063, 75.966, 119.012
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-5NB / 5'-amino-8-bromo-5'-deoxyadenosine


Mass: 345.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13BrN6O3
#3: Chemical ChemComp-5CI / 8-bromo-5'-{[3-carboxy-2-(carboxymethyl)-2-hydroxypropanoyl]amino}-5'-deoxyadenosine


Mass: 519.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19BrN6O9
#4: Chemical ChemComp-CIT / CITRIC ACID


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


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.3 Å3/Da / Density % sol: 46.42 %
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: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 30, 2008
RadiationMonochromator: Asymmetric Laue 001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.34→64.02 Å / Num. obs: 11540 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 %
Reflection shellResolution: 2.34→2.47 Å / Redundancy: 3.8 % / % possible all: 99.6

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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: 2.3801→37.983 Å / SU ML: 0.35 / σ(F): 1.3 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2458 338 2.92 %
Rwork0.2074 --
obs0.2085 11540 97.36 %
all-23290 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.533 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9381 Å20 Å2-0 Å2
2--10.4781 Å20 Å2
3----11.4162 Å2
Refinement stepCycle: LAST / Resolution: 2.3801→37.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 65 81 2159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052182
X-RAY DIFFRACTIONf_angle_d1.0472965
X-RAY DIFFRACTIONf_dihedral_angle_d13.181780
X-RAY DIFFRACTIONf_chiral_restr0.152322
X-RAY DIFFRACTIONf_plane_restr0.003379
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3801-2.56380.38591340.26894303X-RAY DIFFRACTION100
2.5638-2.82180.30051330.23294301X-RAY DIFFRACTION100
2.8218-3.22990.2981500.21524263X-RAY DIFFRACTION100
3.2299-4.06860.1907860.18913821X-RAY DIFFRACTION88
4.0686-37.98770.21031290.19574293X-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)
11.27-0.5545-0.62211.07380.15780.3821-0.1436-0.45450.02020.15150.13040.0663-0.1031-0.12950.03330.43380.12690.05560.5008-0.1080.207213.622524.845122.7321
21.00050.04850.02691.08290.21492.93890.0948-0.04430.06730.0966-0.11310.16-0.0928-0.28090.02160.1040.06080.03170.2067-0.01170.089718.836313.6491-1.449
30.1296-0.2118-0.18880.27040.27960.2572-0.15150.04880.0131-0.10290.00180.10020.0393-0.28050.09850.27490.03540.03450.3632-0.03380.262118.879815.26787.2611
40.32260.04310.00781.3720.50140.3813-0.03740.04920.096-0.0893-0.08190.07150.0469-0.03690.0750.42870.1721-0.06690.5138-0.22290.395330.16124.855215.1456
58.72260.9921-5.58821.7511-1.97154.6694-0.3698-0.50360.38220.3339-0.27970.52790.9005-0.05460.37710.55580.0004-0.0310.5401-0.13030.33116.6459.329311.6875
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 401:481)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 303:303)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 301:302)

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