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- PDB-8of3: Structure of the apoform of ALDEHYDE DEHYDROGENASE 5F1 (ALDH5F1) ... -

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Basic information

Entry
Database: PDB / ID: 8of3
TitleStructure of the apoform of ALDEHYDE DEHYDROGENASE 5F1 (ALDH5F1) from the moss Physcomitrium patens
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
TRIETHYLENE GLYCOL / Succinate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesPhyscomitrium patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.348 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
Palacky University in OlomoucJG_2020_001 Czech Republic
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 13, 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)111,79022
Polymers109,4092
Non-polymers2,38020
Water22,1401229
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)223,58044
Polymers218,8194
Non-polymers4,76140
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
Buried area32570 Å2
ΔGint-148 kcal/mol
Surface area62570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)212.689, 212.689, 186.742
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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: 54704.727 Da / Num. of mol.: 2 / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physcomitrium patens (plant) / Gene: PHYPA_030493
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2K1ICJ7

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Non-polymers , 6 types, 1249 molecules

#2: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1229 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.72 Å3/Da / Density % sol: 66.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7.5 / Details: 1.7M LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.99187 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99187 Å / Relative weight: 1
ReflectionResolution: 1.34→131.14 Å / Num. obs: 241670 / % possible obs: 68 % / Redundancy: 20 % / CC1/2: 0.998 / Rmerge(I) obs: 0.156 / Net I/σ(I): 15.6
Reflection shellResolution: 1.34→1.5 Å / Rmerge(I) obs: 1.8 / Num. unique obs: 12083 / CC1/2: 0.628

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Processing

Software
NameClassification
PHASERphasing
BUSTERrefinement
autoPROCdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.348→131.14 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU R Cruickshank DPI: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.05 / SU Rfree Blow DPI: 0.051 / SU Rfree Cruickshank DPI: 0.049
Details: HYDROGENS WERE FULLY REFINED WITH FULL OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1641 12136 5.02 %RANDOM
Rwork0.1486 ---
obs0.1494 241670 68.6 %-
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1-0.1105 Å20 Å20 Å2
2--0.1105 Å20 Å2
3----0.2211 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.348→131.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7536 0 165 1229 8930
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01216043HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1829177HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4813SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2503HARMONIC5
X-RAY DIFFRACTIONt_it16043HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.72
X-RAY DIFFRACTIONt_other_torsion14.56
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1023SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16657SEMIHARMONIC4
LS refinement shellResolution: 1.35→1.44 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.264 242 5.01 %
Rwork0.2436 4592 -
all0.2446 4834 -
obs--7.95 %
Refinement TLS params.

Method: refined / 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)
10.0830.0553-0.02050.0643-0.0260.29780.0111-0.0001-0.01180.0020.0076-0.0156-0.0220.0715-0.0188-0.1544-0.00490.0092-0.1026-0.0031-0.12464.9093-55.960913.731
20.0774-0.04570.0830.1028-0.10450.1773-0.0038-0.0132-0.00960.00690.0163-0.0029-0.062-0.0515-0.0126-0.12310.02370.0073-0.11340.0054-0.1359-34.633-42.91530.9021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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