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- PDB-2i2c: Crystal structure of LmNADK1 -

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Basic information

Entry
Database: PDB / ID: 2i2c
TitleCrystal structure of LmNADK1
ComponentsProbable inorganic polyphosphate/ATP-NAD kinase 1
KeywordsTRANSFERASE / NADP bound crystal structure of LmNADK1
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-DTA / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPoncet-Montange, G. / 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
DepositionAug 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 14, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Aug 30, 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: Probable inorganic polyphosphate/ATP-NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8043
Polymers31,0451
Non-polymers7592
Water2,396133
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)127,21612
Polymers124,1814
Non-polymers3,0358
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 area14050 Å2
ΔGint-33 kcal/mol
Surface area39950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.070, 75.297, 118.650
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 / PolyP / /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 EGD-e (bacteria)
Species: Listeria monocytogenes / Strain: EGD-E / Gene: ppnK1 / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / 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: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.4
Details: 0.3 M POTASSIUM CHLORIDE, 50 MM TRI-SODIUM CITRATE DIHYDRATE, 15-20% W/V POLYETHYLENE GLYCOL 400, pH 5.4, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.85→25.3 Å / Num. obs: 22941 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 17.3
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 1.9 / % possible all: 93.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I2B

2i2b


Resolution: 1.85→23.29 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.3 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1240 5.1 %RANDOM
Rwork0.191 ---
all0.192 24181 --
obs0.192 22941 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.272 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2--1.88 Å20 Å2
3----2.44 Å2
Refinement stepCycle: LAST / Resolution: 1.85→23.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2073 0 51 133 2257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212251
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.9643045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.2685268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.94622.692104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97715382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5011517
X-RAY DIFFRACTIONr_chiral_restr0.1520.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021690
X-RAY DIFFRACTIONr_nbd_refined0.1970.2997
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21470
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2550.2150
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.220
X-RAY DIFFRACTIONr_mcbond_it0.4241.51382
X-RAY DIFFRACTIONr_mcangle_it0.68322137
X-RAY DIFFRACTIONr_scbond_it0.88331021
X-RAY DIFFRACTIONr_scangle_it1.1954.5905
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 93 -
Rwork0.298 1501 -
obs-1594 90.06 %
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)
13.05750.2503-1.65181.19591.16086.7993-0.1134-0.17090.04890.03980.0395-0.0018-0.0871-0.19920.0739-0.03390.05860.03270.0087-0.0569-0.061611.152523.390121.9517
22.61670.6692-0.83540.26090.13471.6186-0.0244-0.49060.2080.02080.168-0.0704-0.34170.3116-0.14360.21540.09480.05480.1747-0.08830.076921.937926.549626.0052
33.67911.47980.162213.70550.83565.450.0695-0.52570.08410.5646-0.18220.1085-0.0792-0.11610.1127-0.1129-0.02440.0047-0.0415-0.0642-0.179731.491613.924616.7602
41.4395-0.1313-0.04761.98080.352.48410.03820.08420.0948-0.159-0.07250.2802-0.1094-0.37610.0343-0.14140.0329-0.0085-0.10210.0033-0.121617.436313.4379-4.5821
55.3316-1.9743-4.392115.81039.63077.8670.0661-1.8393-1.22171.2789-0.54450.05960.4259-0.85670.47840.034-0.01350.04280.02270.05850.038518.08418.883310.9013
6101.0535-9.0239-4.258488.7964-28.74429.81951.9226-1.5164-1.36530.3358-1.57010.18042.866-0.3855-0.35250.0073-0.0039-0.00470.00230.01590.011517.920235.368815.6165
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 DIFFRACTION5A273
7X-RAY DIFFRACTION6A301

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