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- PDB-5x5t: Crystal structure of alpha-ketoglutarate semialdehyde dehydrogena... -

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Basic information

Entry
Database: PDB / ID: 5x5t
TitleCrystal structure of alpha-ketoglutarate semialdehyde dehydrogenase (KGSADH) from Azospirillum brasilense
ComponentsAlpha-ketoglutaric semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / alpha-ketogluratare semialdehyde dehydrogenase
Function / homology
Function and homology information


2,5-dioxovalerate dehydrogenase / 2,5-dioxovalerate dehydrogenase (NADP+) activity / succinate-semialdehyde dehydrogenase (NAD+) / L-arabinose catabolic process to 2-oxoglutarate / succinate-semialdehyde dehydrogenase (NAD+) activity / NADP+ binding / NAD+ binding / protein tetramerization
Similarity search - Function
Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-ketoglutaric semialdehyde dehydrogenase 1
Similarity search - Component
Biological speciesAzospirillum brasilense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSon, H.-F. / Kim, K.-J.
CitationJournal: Sci Rep / Year: 2017
Title: Structural insights into the production of 3-hydroxypropionic acid by aldehyde dehydrogenase from Azospirillum brasilense.
Authors: Son, H.F. / Park, S. / Yoo, T.H. / Jung, G.Y. / Kim, K.J.
History
DepositionFeb 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Alpha-ketoglutaric semialdehyde dehydrogenase
B: Alpha-ketoglutaric semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8063
Polymers107,7142
Non-polymers921
Water7,674426
1
A: Alpha-ketoglutaric semialdehyde dehydrogenase
B: Alpha-ketoglutaric semialdehyde dehydrogenase
hetero molecules

A: Alpha-ketoglutaric semialdehyde dehydrogenase
B: Alpha-ketoglutaric semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,6136
Polymers215,4284
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Buried area18070 Å2
ΔGint-63 kcal/mol
Surface area58830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.040, 129.040, 118.093
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11B-727-

HOH

21B-784-

HOH

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Components

#1: Protein Alpha-ketoglutaric semialdehyde dehydrogenase / alphaKGSA dehydrogenase / 2 / 5-dioxovalerate dehydrogenase / 2-oxoglutarate semialdehyde ...alphaKGSA dehydrogenase / 2 / 5-dioxovalerate dehydrogenase / 2-oxoglutarate semialdehyde dehydrogenase / Succinate-semialdehyde dehydrogenase [NAD(+)] / SSDH


Mass: 53857.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azospirillum brasilense (bacteria) / Gene: araE / Production host: Escherichia coli (E. coli)
References: UniProt: Q1JUP4, 2,5-dioxovalerate dehydrogenase, succinate-semialdehyde dehydrogenase (NAD+)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 16% polyethylene glycol 3350, 0.1 M sodium cacodylate pH 6.5, and 0.2 M Magnesium chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.25→129.1 Å / Num. obs: 43134 / % possible obs: 95.1 % / Redundancy: 3.4 % / Net I/σ(I): 27.63
Reflection shellResolution: 2.25→2.29 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2W8R

2w8r


Resolution: 2.25→30.606 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.605 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.309 / ESU R Free: 0.234
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2268 5 %RANDOM
Rwork0.1744 ---
obs0.1777 43134 95.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 89.08 Å2 / Biso mean: 30.362 Å2 / Biso min: 16.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2---0.54 Å20 Å2
3---1.07 Å2
Refinement stepCycle: final / Resolution: 2.25→30.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7096 0 6 426 7528
Biso mean--38.6 33.43 -
Num. residues----952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0197255
X-RAY DIFFRACTIONr_bond_other_d0.0020.027058
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.9639881
X-RAY DIFFRACTIONr_angle_other_deg1.037316196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7015950
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.4923.425292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14151118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6411556
X-RAY DIFFRACTIONr_chiral_restr0.1020.21129
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218324
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021604
LS refinement shellResolution: 2.252→2.31 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 167 -
Rwork0.217 3141 -
all-3308 -
obs--94.27 %

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