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- PDB-9kok: Crystal structure of ExaC, an NAD+-dependent aldehyde dehydrogena... -

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Basic information

Entry
Database: PDB / ID: 9kok
TitleCrystal structure of ExaC, an NAD+-dependent aldehyde dehydrogenase, from Pseudomonas aeruginosa
ComponentsNAD+ dependent aldehyde dehydrogenase ExaC
KeywordsOXIDOREDUCTASE / ExaC / crystal structure / NAD+-dependent aldehyde dehydrogenase
Function / homology
Function and homology information


aldehyde dehydrogenase [NAD(P)+] activity / oxidoreductase activity / nucleotide binding
Similarity search - Function
Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD+ dependent aldehyde dehydrogenase ExaC
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsLee, J.Y. / Ko, J.H. / Jeong, K.H. / Son, S.B.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2020R1F1A1072808 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Structural analysis of ExaC, an NAD + -dependent aldehyde dehydrogenase, from Pseudomonas aeruginosa.
Authors: Ko, J.H. / Jeong, K.H. / Son, S.B. / Lee, J.Y.
History
DepositionNov 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD+ dependent aldehyde dehydrogenase ExaC
B: NAD+ dependent aldehyde dehydrogenase ExaC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,89510
Polymers110,1512
Non-polymers1,7448
Water11,151619
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10300 Å2
ΔGint-68 kcal/mol
Surface area33040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.066, 94.066, 238.496
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein NAD+ dependent aldehyde dehydrogenase ExaC


Mass: 55075.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: exaC, PA1984 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9I2C4
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 619 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 0.05M Magnesium chloride, 0.1M HEPES pH 7.5, and 30% (v/v) PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 48623 / % possible obs: 99.7 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 38.85
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.11 / Num. unique obs: 2378

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→19.87 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1889 2011 4.15 %
Rwork0.1321 --
obs0.1345 48441 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7714 0 114 619 8447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098048
X-RAY DIFFRACTIONf_angle_d1.06610963
X-RAY DIFFRACTIONf_dihedral_angle_d11.7541143
X-RAY DIFFRACTIONf_chiral_restr0.061212
X-RAY DIFFRACTIONf_plane_restr0.0091433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.18821380.12843260X-RAY DIFFRACTION99
2.46-2.530.21991420.12593248X-RAY DIFFRACTION100
2.53-2.60.2241390.1393278X-RAY DIFFRACTION100
2.6-2.690.23611400.13083260X-RAY DIFFRACTION100
2.69-2.780.20611470.14783297X-RAY DIFFRACTION100
2.78-2.890.22421420.1383296X-RAY DIFFRACTION100
2.89-3.020.22191430.14743290X-RAY DIFFRACTION100
3.02-3.180.1831420.14113289X-RAY DIFFRACTION100
3.18-3.380.20531410.1383322X-RAY DIFFRACTION100
3.38-3.640.20291410.12883298X-RAY DIFFRACTION100
3.64-40.17181460.12143339X-RAY DIFFRACTION100
4-4.580.14671450.11143329X-RAY DIFFRACTION99
4.58-5.740.15881480.12743375X-RAY DIFFRACTION99
5.74-19.870.18271570.14683549X-RAY DIFFRACTION100

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