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- PDB-8of1: Structure of ALDH5F1 from moss Physcomitrium patens in complex wi... -

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Basic information

Entry
Database: PDB / ID: 8of1
TitleStructure of ALDH5F1 from moss Physcomitrium patens in complex with NAD+ in the contracted 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 / DI(HYDROXYETHYL)ETHER / Succinate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesPhyscomitrium patens (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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, J. / 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, J. / 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)113,31930
Polymers109,3772
Non-polymers3,94128
Water13,313739
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)226,63860
Polymers218,7554
Non-polymers7,88356
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_445x-y-1/3,-y-2/3,-z+1/31
Buried area37270 Å2
ΔGint-305 kcal/mol
Surface area61240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)212.505, 212.505, 186.740
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: 54688.727 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, 767 molecules

#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-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
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 739 / 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: 3.71 Å3/Da / Density % sol: 66.84 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / 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 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.81→106.25 Å / Num. obs: 77952 / % possible obs: 53.4 % / Redundancy: 20 % / CC1/2: 0.998 / Rmerge(I) obs: 0.132 / Net I/σ(I): 13.9
Reflection shellResolution: 1.81→106.25 Å / Rmerge(I) obs: 1.561 / Num. unique obs: 3898 / CC1/2: 0.838

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Processing

Software
NameClassification
PHASERphasing
BUSTERrefinement
autoPROCdata reduction
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→20.82 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.947 / SU R Cruickshank DPI: 0.327 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.177 / SU Rfree Blow DPI: 0.145 / SU Rfree Cruickshank DPI: 0.143
Details: HYDROGENS WERE FULLY REFINED WITH FULL OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.1941 3989 5.12 %RANDOM
Rwork0.1722 ---
obs0.1733 77836 53.3 %-
Displacement parametersBiso mean: 35.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.6169 Å20 Å20 Å2
2--1.6169 Å20 Å2
3----3.2338 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.81→20.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7542 0 247 739 8528
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00915896HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0728842HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4775SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2475HARMONIC5
X-RAY DIFFRACTIONt_it15896HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.83
X-RAY DIFFRACTIONt_other_torsion15.08
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1018SEMIHARMONIC5
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_contact14843SEMIHARMONIC4
LS refinement shellResolution: 1.81→1.92 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2323 103 6.62 %
Rwork0.2267 1454 -
all0.2271 1557 -
obs--6.64 %
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)
10.24430.1222-0.07430.2543-0.11220.780.08970.03460.12970.03130.0480.0917-0.2453-0.2249-0.1377-0.0450.08320.0332-0.02010.0423-0.075-35.062-42.65230.668
20.286-0.09860.0710.3531-0.07260.72210.06160.1280.0831-0.0914-0.0644-0.1392-0.0660.33120.0027-0.1009-0.04320.04730.1260.0213-0.12855.316-55.32812.998
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|-12-492 }A-12 - 492
2X-RAY DIFFRACTION1{ A|501-504 }A501 - 504
3X-RAY DIFFRACTION2{ B|-9-492 }B-9 - 492
4X-RAY DIFFRACTION2{ B|501-503 }B501 - 503

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