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- PDB-4dy6: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -

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Basic information

Entry
Database: PDB / ID: 4dy6
TitleCrystal structure of NAD kinase 1 from Listeria monocytogenes in complex with 2'-phosphate bis(adenosine)-5'-diphosphate
Componentsinorganic polyphosphate/ATP-NAD kinase 1
KeywordsTRANSFERASE / LMNADK1 / NAD analog / inorganic polyphosphates
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-A22 / CITRIC ACID / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionFeb 28, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionMar 7, 2012ID: 2I2E
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: inorganic polyphosphate/ATP-NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9943
Polymers31,0451
Non-polymers9492
Water1,802100
1
A: inorganic polyphosphate/ATP-NAD kinase 1
hetero molecules

A: inorganic polyphosphate/ATP-NAD kinase 1
hetero molecules

A: inorganic polyphosphate/ATP-NAD kinase 1
hetero molecules

A: inorganic polyphosphate/ATP-NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,97512
Polymers124,1814
Non-polymers3,7948
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 area14080 Å2
ΔGint-54 kcal/mol
Surface area40440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.100, 75.730, 118.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein 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: lmo0968, ppnK1 / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Y8D7, NAD+ kinase
#2: Chemical ChemComp-A22 / [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE / 2'-PHOSPHATE BIS(ADENOSINE)-5'-DIPHOSPHATE


Mass: 756.407 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N10O16P3
#3: Chemical ChemComp-CIT / CITRIC ACID


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


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.3 M potassium chloride, 50 mM tri-sodium citrate dihydrate, 15-20% w/v PEG400, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→63.888 Å / Num. obs: 14651 / % possible obs: 99.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 18.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.2-2.322.10.461.6421519760.4694.5
2.32-2.4630.3242.1598020110.32499.8
2.46-2.633.50.2163.4676919150.216100
2.63-2.843.50.1325.5620517690.132100
2.84-3.113.50.0898.2575216360.089100
3.11-3.483.50.05213.4521314930.05299.9
3.48-4.023.50.03319.6457813260.03399.9
4.02-4.923.40.02225.5385911280.02299.8
4.92-6.963.30.02127.629868960.02199.8
6.96-35.09330.0267.615155010.02697.5

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.5data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I2C

2i2c


Resolution: 2.2→33.55 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 14.244 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.316 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 737 5 %RANDOM
Rwork0.2063 ---
obs0.2085 14651 98.84 %-
all-14823 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 134.95 Å2 / Biso mean: 48.0938 Å2 / Biso min: 17.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2--0.89 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2058 0 62 100 2220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212221
X-RAY DIFFRACTIONr_bond_other_d0.0010.021493
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.9823014
X-RAY DIFFRACTIONr_angle_other_deg1.37833627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3015259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.99223.333105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.59515372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0621514
X-RAY DIFFRACTIONr_chiral_restr0.0740.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022426
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02476
X-RAY DIFFRACTIONr_mcbond_it0.8781.51294
X-RAY DIFFRACTIONr_mcbond_other0.1081.5527
X-RAY DIFFRACTIONr_mcangle_it1.59422095
X-RAY DIFFRACTIONr_scbond_it1.2523927
X-RAY DIFFRACTIONr_scangle_it1.9554.5919
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.446 48 -
Rwork0.326 916 -
all-964 -
obs--90.35 %
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)
11.5106-0.5072-1.2330.23030.83133.374-0.0409-0.0698-0.003-0.0154-0.0048-0.04130.0707-0.22930.04580.23770.04110.05110.211-0.05730.127111.12123.60821.806
26.2814-0.5664-4.574-0.37680.80530.70020.2843-1.43750.6391-0.46010.1535-0.4011-0.09431.0377-0.43780.4769-0.01880.27590.3527-0.20620.216922.44326.57525.648
30.04311.6885-0.52138.9351.40933.78010.065-0.01430.04350.50720.00330.15310.06060.0131-0.06830.2401-0.00510.02180.2228-0.03880.143331.6514.11416.878
40.1405-0.2111-0.05330.37450.18251.6330.07370.03640.0365-0.0246-0.08840.01820.0086-0.14110.01460.22450.02870.01960.1914-0.00970.197817.77513.447-4.398
50.7272-4.0958-0.7029-8.29560.08370.3465-0.8408-0.75230.49730.86060.7182-0.2840.4262-0.36820.12260.8782-0.23870.09450.7934-0.26740.173819.9311.8712.146
60.02620.06420.05440.09490.1280.43650.0153-0.00030.0144-0.0102-0.00210.0279-0.0051-0.0274-0.01330.21480.0080.00360.1764-0.00150.20119.003915.65092.9232
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 76
2X-RAY DIFFRACTION2A77 - 97
3X-RAY DIFFRACTION2A245 - 251
4X-RAY DIFFRACTION3A252 - 263
5X-RAY DIFFRACTION4A98 - 244
6X-RAY DIFFRACTION5A301 - 302
7X-RAY DIFFRACTION6A401 - 494

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