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- PDB-8ofm: Structure of the ALDEHYDE DEHYDROGENASE 5F1 (ALDH5F1) from the mo... -

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Basic information

Entry
Database: PDB / ID: 8ofm
TitleStructure of the ALDEHYDE DEHYDROGENASE 5F1 (ALDH5F1) from the moss Physcomitrium patens in complex with NAD in an extended conformation
ComponentsSuccinate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / NAD+ binding / Succinate-semialdehyde dehydrogenase / ALDH5
Function / homology
Function and homology information


succinate-semialdehyde dehydrogenase (NAD+) / succinate-semialdehyde dehydrogenase (NAD+) activity / gamma-aminobutyric acid catabolic process / nucleotide binding / mitochondrion
Similarity search - Function
Succinate semialdehyde dehydrogenase / : / 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 / Succinate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesPhyscomitrium patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.831 Å
AuthorsMorera, S. / Kopecny, D. / Vigouroux, A.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
Czech Science Foundation21-07661S Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicCZ.02.1.01/0.0/0.0/16_019/0000827 Czech Republic
Other governmentJG_2020_001
CitationJournal: To Be Published
Title: A study on abiotic stress responses of aldehyde dehydrogenase (ALDH) superfamilies in moss and barley focused on members linked to the GABA shunt pathway
Authors: Kopecny, D.J. / Belicek, D. / Vigouroux, A. / Luptakova, E. / Koncitikova, R. / von Schwartzenberg, K. / Cavar Zeljkovic, S. / Supikova, K. / Gruz, J. / Valarik, M. / Bergougnoux, V. / ...Authors: Kopecny, D.J. / Belicek, D. / Vigouroux, A. / Luptakova, E. / Koncitikova, R. / von Schwartzenberg, K. / Cavar Zeljkovic, S. / Supikova, K. / Gruz, J. / Valarik, M. / Bergougnoux, V. / Kopecny, D. / Morera, S. / Kopecna, M.
History
DepositionMar 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Succinate-semialdehyde dehydrogenase
B: Succinate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,65337
Polymers109,3772
Non-polymers4,27535
Water12,592699
1
A: Succinate-semialdehyde dehydrogenase
B: Succinate-semialdehyde dehydrogenase
hetero molecules

A: Succinate-semialdehyde dehydrogenase
B: Succinate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,30674
Polymers218,7554
Non-polymers8,55170
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
Buried area39920 Å2
ΔGint-519 kcal/mol
Surface area61170 Å2
Unit cell
Length a, b, c (Å)212.309, 212.309, 187.344
Angle α, β, γ (deg.)90, 90, 120
Int Tables number155
Space group name H-MH32

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Succinate-semialdehyde dehydrogenase


Mass: 54688.727 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrium patens (plant) / Gene: PHYPA_030493 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2K1ICJ7

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Non-polymers , 5 types, 734 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / 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: 2.48 Å3/Da / Density % sol: 50.34 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: lithium sulfate, sodium succinate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.82→131.2 Å / Num. obs: 103740 / % possible obs: 73.4 % / Redundancy: 20 % / CC1/2: 0.998 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.021 / Net I/σ(I): 14.5
Reflection shellResolution: 1.82→2 Å / Rmerge(I) obs: 2.207 / Num. unique obs: 5187 / CC1/2: 0.601

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
STARANISOdata scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.831→26.63 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.167 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.126 / SU Rfree Blow DPI: 0.115 / SU Rfree Cruickshank DPI: 0.114
RfactorNum. reflection% reflectionSelection details
Rfree0.196 5168 -RANDOM
Rwork0.1731 ---
obs0.1743 103682 73.4 %-
Displacement parametersBiso mean: 32.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.049 Å20 Å20 Å2
2---0.049 Å20 Å2
3---0.0981 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.831→26.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7542 0 261 699 8502
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00815923HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0828879HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4793SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2489HARMONIC5
X-RAY DIFFRACTIONt_it15923HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1021SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact14898SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.94
X-RAY DIFFRACTIONt_other_torsion14.17
LS refinement shellResolution: 1.831→1.96 Å
RfactorNum. reflection% reflection
Rfree0.2848 103 -
Rwork0.253 --
obs--8.18 %
Refinement TLS params.

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)
10.23410.1202-0.06060.1589-0.08060.53910.0112-0.012-0.044-0.0120.01370.1235-0.0440.1235-0.0248-0.0687-0.00590.01270.0066-0.0113-0.03115.3172-55.222113.0147
20.1727-0.08250.12660.2522-0.12270.3393-0.01840.0046-0.09830.00460.0249-0.1022-0.0983-0.1022-0.0064-0.03430.03580.00730.0026-0.0009-0.042-34.9958-42.613530.4234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-12 - 492
2X-RAY DIFFRACTION1{ A|* }A587 - 581
3X-RAY DIFFRACTION2{ B|* }B-9 - 492
4X-RAY DIFFRACTION2{ B|* }B581 - 587

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