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- PDB-8co4: Crystal structure of apo S-nitrosoglutathione reductase from Arab... -

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Basic information

Entry
Database: PDB / ID: 8co4
TitleCrystal structure of apo S-nitrosoglutathione reductase from Arabidopsis thalina
ComponentsAlcohol dehydrogenase class-3
KeywordsOXIDOREDUCTASE / nitrosoglutathione reductase / alcohol dehydrogenase class III / metalloprotein / zinc-binding enzyme / Rossman fold
Function / homology
Function and homology information


S-(hydroxymethyl)glutathione dehydrogenase / S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD(P)+) activity / formaldehyde catabolic process / alcohol dehydrogenase (NAD+) activity, zinc-dependent / : / alcohol dehydrogenase / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / zinc ion binding / cytosol
Similarity search - Function
Alcohol dehydrogenase class III / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Alcohol dehydrogenase class-3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFermani, S. / Fanti, S. / Carloni, G. / Rossi, J. / Falini, G. / Zaffagnini, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Plant J. / Year: 2024
Title: Structural and biochemical characterization of Arabidopsis alcohol dehydrogenases reveals distinct functional properties but similar redox sensitivity.
Authors: Meloni, M. / Rossi, J. / Fanti, S. / Carloni, G. / Tedesco, D. / Treffon, P. / Piccinini, L. / Falini, G. / Trost, P. / Vierling, E. / Licausi, F. / Giuntoli, B. / Musiani, F. / Fermani, S. / Zaffagnini, M.
History
DepositionFeb 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alcohol dehydrogenase class-3
B: Alcohol dehydrogenase class-3
C: Alcohol dehydrogenase class-3
D: Alcohol dehydrogenase class-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,72930
Polymers162,9874
Non-polymers2,74226
Water18,7361040
1
A: Alcohol dehydrogenase class-3
B: Alcohol dehydrogenase class-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,39919
Polymers81,4932
Non-polymers1,90617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-72 kcal/mol
Surface area30020 Å2
MethodPISA
2
C: Alcohol dehydrogenase class-3
D: Alcohol dehydrogenase class-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,33011
Polymers81,4932
Non-polymers8369
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-96 kcal/mol
Surface area30680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.600, 93.927, 167.484
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Alcohol dehydrogenase class-3 / Alcohol dehydrogenase class-III / Glutathione-dependent formaldehyde dehydrogenase / FALDH / FDH / ...Alcohol dehydrogenase class-III / Glutathione-dependent formaldehyde dehydrogenase / FALDH / FDH / GSH-FDH / S-(hydroxymethyl)glutathione dehydrogenase


Mass: 40746.680 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ADH2, ADHIII, FDH1, At5g43940, MRH10.4 / Organ: cytoplasm / Plasmid: pET-28a / Production host: Escherichia coli (E. coli)
References: UniProt: Q96533, alcohol dehydrogenase, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor, S-(hydroxymethyl)glutathione dehydrogenase

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Non-polymers , 6 types, 1066 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1040 / 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: 2.14 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Na(CH3COO), 0.1M Tris-HCl, 20% w/v PEG 4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→81.92 Å / Num. obs: 110542 / % possible obs: 99.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 22.24 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.096 / Rrim(I) all: 0.167 / Net I/σ(I): 7.6
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 1.012 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5434 / CC1/2: 0.739 / Rpim(I) all: 0.717 / Rrim(I) all: 1.245 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PHENIX1.19rc7_4070refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→81.92 Å / SU ML: 0.2048 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.8803
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2105 5383 4.88 %random
Rwork0.161 104990 --
obs0.1634 110373 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.58 Å2
Refinement stepCycle: LAST / Resolution: 1.9→81.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11396 0 155 1040 12591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010211935
X-RAY DIFFRACTIONf_angle_d1.04516162
X-RAY DIFFRACTIONf_chiral_restr0.06821836
X-RAY DIFFRACTIONf_plane_restr0.00792073
X-RAY DIFFRACTIONf_dihedral_angle_d9.66171723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.30311900.23523511X-RAY DIFFRACTION99.78
1.92-1.940.2531390.22733413X-RAY DIFFRACTION99.58
1.94-1.970.26881690.21953497X-RAY DIFFRACTION99.73
1.97-1.990.28961900.20893434X-RAY DIFFRACTION99.67
1.99-2.020.24181860.19293469X-RAY DIFFRACTION99.81
2.02-2.050.29421820.193458X-RAY DIFFRACTION99.92
2.05-2.080.24012000.17443419X-RAY DIFFRACTION99.78
2.08-2.110.22931680.16833483X-RAY DIFFRACTION99.81
2.11-2.140.22651920.16613455X-RAY DIFFRACTION99.84
2.14-2.170.24442010.16893435X-RAY DIFFRACTION99.67
2.17-2.210.23711760.16633467X-RAY DIFFRACTION99.84
2.21-2.250.21731760.16943474X-RAY DIFFRACTION99.92
2.25-2.30.24291420.16543518X-RAY DIFFRACTION99.78
2.3-2.340.21621770.16523497X-RAY DIFFRACTION99.73
2.34-2.390.24341470.1673512X-RAY DIFFRACTION99.84
2.39-2.450.24551760.17253448X-RAY DIFFRACTION99.75
2.45-2.510.24191760.16893458X-RAY DIFFRACTION99.59
2.51-2.580.23612040.16153468X-RAY DIFFRACTION99.76
2.58-2.650.25282000.17483444X-RAY DIFFRACTION99.62
2.65-2.740.21671590.17373546X-RAY DIFFRACTION99.62
2.74-2.840.21471880.16373480X-RAY DIFFRACTION99.78
2.84-2.950.2161530.16723531X-RAY DIFFRACTION99.97
2.95-3.090.20451800.17033503X-RAY DIFFRACTION99.95
3.09-3.250.24061920.16993519X-RAY DIFFRACTION99.89
3.25-3.450.20151680.1583539X-RAY DIFFRACTION99.92
3.45-3.720.17081990.1463532X-RAY DIFFRACTION100
3.72-4.090.15532050.13743520X-RAY DIFFRACTION99.95
4.09-4.690.16931770.1243590X-RAY DIFFRACTION100
4.69-5.90.16351680.143628X-RAY DIFFRACTION99.97
5.9-81.920.19932030.15433742X-RAY DIFFRACTION99.52

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