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- PDB-7qvs: Pseudomonas aeruginosa nicotinamide adenine dinucleotide kinase (... -

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Basic information

Entry
Database: PDB / ID: 7qvs
TitlePseudomonas aeruginosa nicotinamide adenine dinucleotide kinase (NADK) structure in complex with NADP
ComponentsNAD kinase
KeywordsSTRUCTURAL PROTEIN / kinases / antibiotics / inhibitors / drug discovery
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
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
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PHOSPHATE ION / NAD kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRahimova, R. / Gelin, M. / Labesse, G. / Lionne, C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE18-0011-02 France
CitationJournal: Febs J. / Year: 2023
Title: Structure-based design, synthesis and biological evaluation of a NAD + analogue targeting Pseudomonas aeruginosa NAD kinase.
Authors: Rahimova, R. / Nogaret, P. / Huteau, V. / Gelin, M. / Clement, D.A. / Labesse, G. / Pochet, S. / Blanc-Potard, A.B. / Lionne, C.
History
DepositionJan 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD kinase
B: NAD kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1826
Polymers66,5052
Non-polymers1,6774
Water3,981221
1
A: NAD kinase
B: NAD kinase
hetero molecules

A: NAD kinase
B: NAD kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,36312
Polymers133,0104
Non-polymers3,3548
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/41
Buried area17030 Å2
ΔGint-207 kcal/mol
Surface area40290 Å2
Unit cell
Length a, b, c (Å)88.770, 88.770, 174.247
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c

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Components

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


Mass: 33252.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: ppnK, nadK, CAZ10_03565, CSB93_3290, DY940_12450, E4V10_28275, IPC116_13595, IPC1295_03320, IPC1316_10105, IPC1323_13200, IPC1339_13410, IPC1598_02670, IPC29_18225, IPC614_04535, IPC737_03790, ...Gene: ppnK, nadK, CAZ10_03565, CSB93_3290, DY940_12450, E4V10_28275, IPC116_13595, IPC1295_03320, IPC1316_10105, IPC1323_13200, IPC1339_13410, IPC1598_02670, IPC29_18225, IPC614_04535, IPC737_03790, IPC90_26155, NCTC12924_04243, PAMH19_1983, RW109_RW109_02738
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A071KS55, NAD+ kinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 mM Tris pH 8.5, 0.8 mM AmSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00 A
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→79.097 Å / Num. obs: 31752 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 31.47 Å2 / CC1/2: 1 / Net I/σ(I): 39.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 15 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 5.4 / Num. unique obs: 1551 / CC1/2: 1 / Rpim(I) all: 0.131 / Rrim(I) all: 0.669 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AN1

2an1


Resolution: 2.3→29.59 Å / SU ML: 0.2771 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6035
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 1570 4.95 %RANDOM
Rwork0.197 30136 --
obs0.1989 31706 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.74 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4247 0 106 221 4574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01284531
X-RAY DIFFRACTIONf_angle_d1.51656185
X-RAY DIFFRACTIONf_chiral_restr0.2127719
X-RAY DIFFRACTIONf_plane_restr0.0127779
X-RAY DIFFRACTIONf_dihedral_angle_d17.37471621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.28641460.22542649X-RAY DIFFRACTION98.97
2.37-2.460.27651560.21012680X-RAY DIFFRACTION100
2.46-2.560.25651370.20872685X-RAY DIFFRACTION100
2.56-2.670.26341410.21982718X-RAY DIFFRACTION100
2.67-2.810.25611550.21582662X-RAY DIFFRACTION100
2.81-2.990.25871430.20912732X-RAY DIFFRACTION100
2.99-3.220.21611380.20182730X-RAY DIFFRACTION99.97
3.22-3.550.22291620.18422719X-RAY DIFFRACTION100
3.55-4.060.23851290.17272759X-RAY DIFFRACTION99.21
4.06-5.110.18391180.16912820X-RAY DIFFRACTION100
5.11-29.590.2421450.22122982X-RAY DIFFRACTION99.94
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)
10.2457461842380.5646557578390.7323523117942.007468389231.281701305062.42649109751-0.2714904707750.316468974914-0.256376763937-0.525185436844-0.00622053177130.3271252877340.41137703465-0.8047021250970.4561060746930.82576659138-0.3708322438140.03708839017270.772411677489-0.2863726204430.582960335555-20.5174702523-14.1126854137-7.58159186344
21.230107543170.6734888781980.02601314986032.152816860651.727819123042.5445968668-0.3450302457390.421760477285-0.310906440578-0.5452402289480.03119338055550.07163583979670.313200521757-0.3643710874170.2032199138320.509775223545-0.1012885233330.08306534195720.328766253247-0.09656107624550.35177971429-13.0278693352-6.984048847150.451344797331
32.25572342480.228506753644-0.7328483919381.794569415010.03190195662012.92425963296-0.107070861927-0.0597524687661-0.246208096038-0.09249250890730.03847412641470.0596873026970.231219700093-0.2481025422090.05274370432760.17916844194-0.00208011463084-0.003135824758490.1708635615590.02056915847960.210553218139-18.25597027240.17311652937222.1410649532
44.360049570660.503252288834-2.417350490092.210712073231.025808113182.131202708610.077721974613-0.881948629643-0.1400911102390.4936664491140.1705375973570.221628800917-0.0591249345691-0.561840370717-0.1856367655010.5303276875950.0748780100590.1095484209051.283525340250.2322516607040.532165381556-47.630714090717.129664458851.149306481
53.0518131537-0.0110036629053-1.965419363971.23013033883-0.1770595835452.4699837494-0.0607187290284-0.799338373912-0.03816295937740.4760859615850.1184364149910.342118315332-0.0924799705321-0.743733239594-0.05288896468940.4409339047970.1255437233750.09248121224340.9628593877110.05383007975390.462020701684-46.55089172421.541010015143.6745448261
61.698720542730.4091159153260.6745079369851.52994020680.3484906604482.517255685170.0314644651772-0.03589176107160.0562533177742-0.07968732681770.02082057233310.187068782823-0.0619727146555-0.395205032281-0.02109132189430.15767138990.02661761538244.55112970501E-50.2854578656760.0506171854560.228796497957-36.698627654219.058951216120.6110864236
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 55 )AA3 - 551 - 53
22chain 'A' and (resid 56 through 127 )AA56 - 12754 - 125
33chain 'A' and (resid 128 through 291 )AA128 - 291126 - 289
44chain 'B' and (resid 3 through 32 )BB3 - 321 - 30
55chain 'B' and (resid 33 through 125 )BB33 - 12531 - 115
66chain 'B' and (resid 126 through 293 )BB126 - 293116 - 283

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