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- PDB-7uyy: The crystal structure of the Pseudomonas aeruginosa aldehyde dehy... -

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Basic information

Entry
Database: PDB / ID: 7uyy
TitleThe crystal structure of the Pseudomonas aeruginosa aldehyde dehydrogenase encoded by the PA4189 gene in complex with NADH
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / tetramer / aldehyde dehydrogenase fold / aminoaldehyde dehydrogenase / ALDH27 family
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / organic substance metabolic process
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, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
: / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Probable aldehyde dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGonzalez-Segura, L. / Juarez-Vazquez, A.L. / Munoz-Clares, R.A.
Funding support Mexico, 2items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)283524 Mexico
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)IN220317 Mexico
CitationJournal: Biochem.J. / Year: 2023
Title: The uncharacterized Pseudomonas aeruginosa PA4189 is a novel and efficient aminoacetaldehyde dehydrogenase.
Authors: Fernandez-Silva, A. / Juarez-Vazquez, A.L. / Gonzalez-Segura, L. / Juarez-Diaz, J.A. / Munoz-Clares, R.A.
History
DepositionMay 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Oct 25, 2023Group: 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: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,99144
Polymers110,7972
Non-polymers4,19442
Water9,512528
1
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
hetero molecules

A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,98388
Polymers221,5954
Non-polymers8,38884
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_444x-y-1/3,-y-2/3,-z-2/31
Buried area32900 Å2
ΔGint-183 kcal/mol
Surface area57030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.518, 184.518, 251.136
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-635-

HOH

21B-615-

HOH

31B-766-

HOH

41B-813-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Aldehyde dehydrogenase /


Mass: 55398.633 Da / Num. of mol.: 2
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: PA4189 / Plasmid: pET28b-PA4189 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): Roseta DE3 / References: UniProt: Q9HWJ2

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Non-polymers , 7 types, 570 molecules

#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 528 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.85 Å3/Da / Density % sol: 68.04 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.17 M Lithium Sulfate monohydrate, 0.085 M Tris Hydrochloride pH 8.5, 26.6% w/v Polyethylene Glycol 4000, 15% v/v Glycerol

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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 PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→47.96 Å / Num. obs: 44964 / % possible obs: 99.9 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 20
Reflection shellResolution: 2.7→2.85 Å / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 7.9 / Num. unique obs: 6493

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6B4R

6b4r


Resolution: 2.7→47.92 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 16.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1813 2271 5.05 %
Rwork0.1351 42678 -
obs0.1374 44949 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.33 Å2 / Biso mean: 28.5999 Å2 / Biso min: 4.31 Å2
Refinement stepCycle: final / Resolution: 2.7→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7516 0 262 528 8306
Biso mean--43.73 33.1 -
Num. residues----990
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.760.26641160.176526552771100
2.76-2.830.24641470.156826602807100
2.83-2.90.23481360.145126182754100
2.9-2.980.18461450.142726582803100
2.98-3.060.20281510.142926432794100
3.06-3.160.17761520.14726012753100
3.16-3.280.19621400.138226722812100
3.28-3.410.18571480.138526472795100
3.41-3.560.1681520.129426472799100
3.56-3.750.17751350.124626762811100
3.75-3.980.16161480.123626552803100
3.99-4.290.15131340.11612657279199
4.29-4.720.16261400.107326862826100
4.72-5.410.15871530.126326752828100
5.41-6.810.21761450.155627182863100
6.81-47.920.1611290.15328102939100

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