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- PDB-7mh7: crystal structure of NAD kinase from Pseudomonas aeruginosa PAO1 -

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Basic information

Entry
Database: PDB / ID: 7mh7
Titlecrystal structure of NAD kinase from Pseudomonas aeruginosa PAO1
ComponentsNAD kinase
KeywordsTRANSFERASE / NAD KINASE / CSGID / structural genomics / Center for Structural Genomics of Infectious Diseases
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 / NAD kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsChang, C. / Evdokimova, E. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of NAD kinase from Pseudomonas aeruginosa
Authors: Chang, C. / Evdokimova, E. / Savchenko, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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

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Assembly

Deposited unit
A: NAD kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9252
Polymers32,1811
Non-polymers7431
Water72140
1
A: NAD kinase
hetero molecules

A: NAD kinase
hetero molecules

A: NAD kinase
hetero molecules

A: NAD kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,6998
Polymers128,7254
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation11_656-x+y+1,y,-z+11
Buried area16030 Å2
ΔGint-79 kcal/mol
Surface area41570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.165, 99.165, 121.867
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

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Components

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


Mass: 32181.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: nadK, PA3088 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HZC0, NAD+ kinase
#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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.69 Å3/Da / Density % sol: 54.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M di-ammonium tartrate, 10% MPD, 1.5mM NADP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Oct 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 11351 / % possible obs: 100 % / Redundancy: 48.5 % / Biso Wilson estimate: 35.19 Å2 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.016 / Rrim(I) all: 0.114 / Χ2: 0.99 / Net I/σ(I): 7.9 / Num. measured all: 550309
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6429.62.7825390.6590.5082.8310.924100
2.64-2.6935.62.2855510.7290.3842.3181.0299.8
2.69-2.7438.42.0325530.7630.3292.0590.932100
2.74-2.840.82.0665480.7790.3242.0910.931100
2.8-2.8648.61.8145500.9020.261.8330.941100
2.86-2.93511.5435510.9810.2161.5580.938100
2.93-352.41.1595620.9660.161.170.969100
3-3.0852.80.9375550.980.1290.9460.967100
3.08-3.1752.90.7295530.9870.10.7350.968100
3.17-3.2852.10.6055660.9910.0830.6110.985100
3.28-3.3948.40.4135560.9960.0590.4181.02100
3.39-3.5352.90.3385560.9970.0460.3411.032100
3.53-3.6955.10.2275690.9980.030.2291.04100
3.69-3.8854.80.1825580.9990.0240.1841.027100
3.88-4.1353.40.1435780.9990.020.1451.00999.8
4.13-4.4550.10.0985650.9990.0140.0991.021100
4.45-4.8952.60.085830.9990.0110.0811.025100
4.89-5.6530.0785860.9990.0110.0791.019100
5.6-7.0548.20.0686040.9990.010.0680.992100
7.05-5045.80.0586680.9990.0090.0590.97699.7

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000phasing
SBC-Collectdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AN1.pdb

2an1


Resolution: 2.61→40.62 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2597 509 5.04 %
Rwork0.2157 9591 -
obs0.2179 10100 89.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.89 Å2 / Biso mean: 50.1146 Å2 / Biso min: 7.01 Å2
Refinement stepCycle: final / Resolution: 2.61→40.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 48 40 2280
Biso mean--33.55 32.91 -
Num. residues----290
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.61-2.870.3241680.26411446151455
2.87-3.280.31221620.247826212783100
3.28-4.140.25991310.207526842815100
4.14-40.620.22381480.198128402988100
Refinement TLS params.Method: refined / Origin x: 34.3958 Å / Origin y: 16.998 Å / Origin z: 70.8981 Å
111213212223313233
T0.1307 Å20.0788 Å20.0046 Å2-0.1781 Å2-0.0621 Å2--0.2275 Å2
L1.2821 °20.1499 °2-0.188 °2-2.685 °21.3745 °2--1.9289 °2
S-0.2262 Å °-0.2139 Å °0.2013 Å °0.2674 Å °-0.1457 Å °0.611 Å °0.0315 Å °-0.3197 Å °-0.0077 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 2 through 291)

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