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- PDB-2q5f: Crystal structure of LMNADK1 from Listeria monocytogenes -

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Basic information

Entry
Database: PDB / ID: 2q5f
TitleCrystal structure of LMNADK1 from Listeria monocytogenes
ComponentsProbable inorganic polyphosphate/ATP-NAD kinase 1
KeywordsTRANSFERASE / Mutant
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
Chem-DTA / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (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
DepositionJun 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Oct 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 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.4Apr 3, 2024Group: Refinement description / Category: 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)31,6012
Polymers31,0361
Non-polymers5651
Water1,51384
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)126,4038
Polymers124,1454
Non-polymers2,2584
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 area12680 Å2
ΔGint-60 kcal/mol
Surface area38750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)62.959, 75.088, 118.490
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: 31036.244 Da / Num. of mol.: 1 / Mutation: H223E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Species: Listeria monocytogenes / Strain: EGD-E / Gene: ppnK1 / Plasmid: PET22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8Y8D7, NAD+ kinase
#2: Chemical ChemComp-DTA / (2S,3S,4R,5R,2'S,3'S,4'R,5'R)-2,2'-[DITHIOBIS(METHYLENE)]BIS[5-(6-AMINO-9H-PURIN-9-YL)TETRAHYDROFURAN-3,4-DIOL] / DI-(5'-THIOADENOSINE)


Mass: 564.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O6S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 45.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG400 15-20% w/v, KCitrate 50 mM, KCl 300 mM, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→28.2 Å / Num. all: 22000 / Num. obs: 19663 / % possible obs: 87.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 29.25 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.063 / Net I/σ(I): 20.2
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1644 / % possible all: 51.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB2I2C

Resolution: 1.9→28.2 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.95 / SU B: 8.046 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.175 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22181 589 3 %RANDOM
Rwork0.18815 ---
all0.18914 22528 --
obs0.18914 19066 87.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.827 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2--2.42 Å20 Å2
3----1.92 Å2
Refine analyzeLuzzati coordinate error obs: 0.3036 Å
Refinement stepCycle: LAST / Resolution: 1.9→28.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 38 84 2178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222178
X-RAY DIFFRACTIONr_bond_other_d0.0080.021473
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9762953
X-RAY DIFFRACTIONr_angle_other_deg1.6153.0013552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg21.3755262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.53323.069101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.38515364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.4011515
X-RAY DIFFRACTIONr_chiral_restr0.0890.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022398
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02465
X-RAY DIFFRACTIONr_nbd_refined0.2170.2346
X-RAY DIFFRACTIONr_nbd_other0.2120.21443
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21001
X-RAY DIFFRACTIONr_nbtor_other0.0980.21150
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2920.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6921.51417
X-RAY DIFFRACTIONr_mcbond_other0.0911.5527
X-RAY DIFFRACTIONr_mcangle_it0.84722089
X-RAY DIFFRACTIONr_scbond_it1.4313987
X-RAY DIFFRACTIONr_scangle_it1.64.5861
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 14 -
Rwork0.286 727 -
obs--45.77 %
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)
12.5996-1.1784-1.65321.33431.55237.4694-0.0929-0.1530.05340.12950.00470.0962-0.2181-0.35110.08820.01680.03550.04570.0683-0.0785-0.051410.14624.21422.295
21.74880.0024-0.25140.0614-0.41652.8583-0.0676-0.59120.29020.18220.4443-0.1162-0.19030.5217-0.37670.24430.05340.0520.2732-0.13540.07622.03825.48224.644
34.20771.80730.144813.7472-2.84956.35280.0803-0.38660.25770.6417-0.08270.0884-0.13360.08230.0024-0.0495-0.03890.0174-0.0339-0.0544-0.184931.35214.33316.462
41.27-0.21960.16391.88470.2732.83230.07350.0490.0661-0.1479-0.13930.2741-0.0947-0.39480.0657-0.13940.038-0.0096-0.055-0.014-0.124717.90213.232-4.476
50.0715-1.143-1.1318.264818.057317.8523-0.2015-0.8526-0.64781.965-0.60870.50421.3913-0.26180.81020.1584-0.00370.07460.16520.04360.020717.7148.87611.163
60.11240.09170.14760.4310.50730.62720.0398-0.00960.02220.01290.00470.0367-0.0305-0.0516-0.0445-0.00070.01780.01140.0504-0.00420.015719.10514.5523.179
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 691 - 69
2X-RAY DIFFRACTION2AA74 - 9774 - 97
3X-RAY DIFFRACTION2AA245 - 251245 - 251
4X-RAY DIFFRACTION3AA252 - 263252 - 263
5X-RAY DIFFRACTION4AA98 - 24498 - 244
6X-RAY DIFFRACTION5AB2731
7X-RAY DIFFRACTION6AC274 - 3571 - 84

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