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- PDB-5ejh: Crystal structure of NAD kinase V98S mutant from Listeria monocyt... -

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Basic information

Entry
Database: PDB / ID: 5ejh
TitleCrystal structure of NAD kinase V98S mutant from Listeria monocytogenes
ComponentsNAD kinase 1NAD+ kinase
KeywordsTRANSFERASE / Gram-positive NAD Kinase / allostery / citrate
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 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 / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1 from Listeria monocytogenes: V98S mutant
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: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9693
Polymers31,0331
Non-polymers9362
Water2,594144
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)127,87512
Polymers124,1334
Non-polymers3,7428
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 area13960 Å2
ΔGint-35 kcal/mol
Surface area39300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.759, 75.880, 118.207
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-448-

HOH

21A-536-

HOH

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Components

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


Mass: 31033.225 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
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


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


Mass: 18.015 Da / Num. of mol.: 144 / 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: 45.75 %
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: 1.844→63.856 Å / Num. all: 18435 / Num. obs: 18435 / % possible obs: 95.4 % / Redundancy: 2.7 % / Rpim(I) all: 0.052 / Rrim(I) all: 0.091 / Rsym value: 0.074 / Net I/av σ(I): 7.213 / Net I/σ(I): 10.8 / Num. measured all: 48946
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.112.70.491.5707826510.3470.49295.8
2.11-2.242.70.3312.3673725400.2360.3312.895.9
2.24-2.392.70.2413.2634023850.1710.2413.996.1
2.39-2.582.70.1664.6591122240.1180.1665.595.9
2.58-2.832.70.1116.7547420540.0790.1118.195.7
2.83-3.162.70.07110.2497918500.050.07111.995.2
3.16-3.652.70.04216.3438516470.0290.04217.895.4
3.65-4.472.60.02921.8367313880.020.02924.394.5
4.47-6.322.60.02620.8282910820.0180.02634.794
6.32-37.4282.50.0386.115406140.0290.03841.791.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.21data scaling
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I2A

2i2a


Resolution: 2→31.309 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 1052 3 %
Rwork0.1766 34053 -
obs0.178 18405 95.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.32 Å2 / Biso mean: 34.6543 Å2 / Biso min: 11.06 Å2
Refinement stepCycle: final / Resolution: 2→31.309 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 64 144 2277
Biso mean--52.78 41.81 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072198
X-RAY DIFFRACTIONf_angle_d0.9862979
X-RAY DIFFRACTIONf_chiral_restr0.048318
X-RAY DIFFRACTIONf_plane_restr0.005376
X-RAY DIFFRACTIONf_dihedral_angle_d15.132790
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0910.33321380.26874253439195
2.091-2.20120.29391430.24464220436396
2.2012-2.33910.28511310.22094312444396
2.3391-2.51960.29521350.20234267440296
2.5196-2.7730.22911150.18474268438396
2.773-3.1740.21391520.17474277442995
3.174-3.99760.17751090.14754267437695
3.9976-31.31240.17271290.14544189431894
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)
10.02490.0038-0.01990.00730.00470.0165-0.11-0.2206-0.08230.0554-0.00850.0748-0.0932-0.0251-0.00010.33550.07790.04950.3376-0.09010.25578.749822.50528.7597
20.0472-0.0116-0.00890.0127-0.01820.0214-0.1141-0.10140.10620.0438-0.09930.0833-0.0284-0.0947-0.01490.23930.06610.03550.2705-0.10080.26679.581225.813319.8324
30.00740.001-0.0099-0.0013-0.00410.006-0.0396-0.04170.0537-0.036-0.06910.0233-0.0543-0.0164-0.02280.36960.12450.00210.2075-0.05040.285312.361926.854314.5569
40.00710.01-0.01220.0138-0.01190.0092-0.0226-0.18110.0305-0.01380.0704-0.04020.07880.04830.0450.20860.27840.11810.4685-0.24120.033920.269921.698726.5934
50.03780.0226-0.02960.02850.00040.0620.17070.06440.15590.09080.00570.0818-0.0667-0.10930.03760.20510.08010.03770.218-0.04090.24314.715223.81164.3408
60.0597-0.0308-0.05420.05050.00540.02670.04790.01380.0669-0.0041-0.07750.0629-0.0447-0.0945-0.00060.12910.0299-0.00680.1206-0.0030.135720.959811.1037-3.9973
70.03980.0314-0.00550.0180.00320.00060.13550.0510.0266-0.1351-0.09790.06170.05880.03090.00150.2330.0071-0.02850.15740.01350.12725.51310.817-13.2423
80.0323-0.0084-0.01610.0082-0.01410.06780.07490.12680.0197-0.0453-0.05490.0991-0.1491-0.14220.01870.14830.0716-0.01640.17980.01610.227817.295815.2182-10.4126
90.0019-0.0129-0.00430.05910.0140.0047-0.02340.09910.1592-0.0357-0.04490.18950.0041-0.2141-0.00420.14160.0424-0.0180.3191-0.01680.2688.900513.2957-3.5604
100.006-0.01590.00360.00150.0038-0.00020.1606-0.03020.0982-0.00880.00070.0179-0.0175-0.03940.00020.3592-0.0030.0430.1931-0.0550.29322.592526.448214.8082
110.00180.0015-0.0037-0.0005-0.0020.0038-0.0049-0.05090.05310.0674-0.0389-0.00520.0433-0.0356-00.229-0.0304-0.00120.2332-0.05340.184631.443813.191316.9895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 26 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 54 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 68 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 92 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 93 through 122 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 123 through 184 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 185 through 198 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 199 through 216 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 217 through 238 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 239 through 252 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 253 through 263 )A0

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