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- PDB-5eji: Crystal structure of NAD kinase W78F mutant from Listeria monocyt... -

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Basic information

Entry
Database: PDB / ID: 5eji
TitleCrystal structure of NAD kinase W78F mutant from Listeria monocytogenes in complex with NADP/Mn++/PPi
ComponentsNAD kinase 1
KeywordsTRANSFERASE / Gram-positive NAD Kinase / allostery / citrate
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
CITRIC ACID / : / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PYROPHOSPHATE 2- / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.292 Å
AuthorsPoncet-Montange, G. / Assairi, L. / Gelin, M. / Pochet, S. / Labesse, G.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
Citation
Journal: to be published
Title: Crystal structure of NAD kinase W78F mutant from Listeria monocytogenes in complex with NADP/Mn++/PPi
Authors: Poncet-Montange, G. / Assairi, L. / Gelin, M. / Pochet, S. / Labesse, G.
#1: Journal: To Be Published
Title: Molecular basis of NAD kinase catalysis reveals citrate is an allosteric regulator.
Authors: Poncet-Montange, G. / Assairi, L. / Gelin, M. / Pochet, S. / Labesse, G.
History
DepositionNov 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Advisory / Author supporting evidence / Data collection
Category: diffrn_radiation_wavelength / pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_audit_support.funding_organization
Revision 2.0May 8, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1735
Polymers31,0061
Non-polymers1,1664
Water61334
1
A: NAD kinase 1
hetero molecules

A: NAD kinase 1
hetero molecules

A: NAD kinase 1
hetero molecules

A: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,69120
Polymers124,0254
Non-polymers4,66616
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 area16930 Å2
ΔGint-78 kcal/mol
Surface area38290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.466, 74.389, 119.012
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-434-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NAD kinase 1 / ATP-dependent NAD kinase


Mass: 31006.244 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: nadK1, lmo0968 / Plasmid: pLA15.3.3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8Y8D7, NAD+ kinase

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Non-polymers , 5 types, 38 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#5: Chemical ChemComp-CIT / CITRIC ACID


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


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 50 mM Sodium Bromide, 150 mM tri-sodium citrate dihydrate, pH 5.1-5.4, 14-16% w/v polyethylene glycol 400

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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: Sep 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.829→63.069 Å / Num. all: 13007 / Num. obs: 13007 / % possible obs: 100 % / Redundancy: 4.1 % / Rpim(I) all: 0.039 / Rrim(I) all: 0.079 / Rsym value: 0.061 / Net I/av σ(I): 9.5 / Net I/σ(I): 12.5 / Num. measured all: 53269
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.29-2.414.10.5611.3777218840.3630.5611.9100
2.41-2.564.20.3812734917620.2490.3812.8100
2.56-2.744.20.2343.2694316660.1490.2344.4100
2.74-2.964.10.1794.1646415590.1160.1795.9100
2.96-3.244.20.1057590814210.0670.1059.9100
3.24-3.624.10.05712537113090.0360.05715.6100
3.62-4.184.10.03418.4474311580.0210.03421.5100
4.18-5.1240.02328.340299980.0140.02327.4100
5.12-7.243.90.02423.830737830.0150.02437.599.9
7.24-63.0693.50.02912.816174670.020.02947.299.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.21data scaling
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.292→63.08 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.18 / Phase error: 29.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2369 709 2.93 %
Rwork0.1772 23486 -
obs0.1789 12906 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.75 Å2 / Biso mean: 56.6136 Å2 / Biso min: 13.89 Å2
Refinement stepCycle: final / Resolution: 2.292→63.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2053 0 71 34 2158
Biso mean--57.56 50.71 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082185
X-RAY DIFFRACTIONf_angle_d1.0712963
X-RAY DIFFRACTIONf_chiral_restr0.052319
X-RAY DIFFRACTIONf_plane_restr0.006372
X-RAY DIFFRACTIONf_dihedral_angle_d16.673782
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2916-2.46850.35611560.26774486464294
2.4685-2.71690.25741270.233747574884100
2.7169-3.110.30661570.214447354892100
3.11-3.91830.22521270.160947344861100
3.9183-63.1040.19291420.1547744916100
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)
10.3348-0.0196-0.25010.08010.12160.23570.0359-0.38090.1507-0.0803-0.011-0.03420.0590.10040.00030.50750.05650.03790.5693-0.140.443413.653424.050322.9923
20.35750.0445-0.51650.2385-0.10140.57270.02130.09240.13990.0802-0.07460.1382-0.032-0.0979-0.00490.10690.0578-0.01830.1109-0.02070.169719.407113.6196-1.7224
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 101 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 102 through 264 )A0

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