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- PDB-7aas: Crystal structure of nitrosoglutathione reductase (GSNOR) from Ch... -

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Basic information

Entry
Database: PDB / ID: 7aas
TitleCrystal structure of nitrosoglutathione reductase (GSNOR) from Chlamydomonas reinhardtii
ComponentsS-(hydroxymethyl)glutathione dehydrogenase
KeywordsOXIDOREDUCTASE / Alcohol dehydrogenase / Zinc-binding dehydrogenase
Function / homology
Function and homology information


S-(hydroxymethyl)glutathione dehydrogenase (NADP+) activity / S-(hydroxymethyl)glutathione dehydrogenase (NAD+) activity / S-(hydroxymethyl)glutathione dehydrogenase / S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity / formaldehyde catabolic process / alcohol dehydrogenase (NAD+) activity / nucleotide binding / 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 / S-(hydroxymethyl)glutathione dehydrogenase
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFermani, S. / Zaffagnini, M. / Falini, G. / Lemaire, S.D.
Funding support Italy, France, 2items
OrganizationGrant numberCountry
Other governmentAlma Idea 2017 Italy
Agence Nationale de la Recherche (ANR)17-CE05-0001 France
CitationJournal: Redox Biol / Year: 2020
Title: Structural and functional insights into nitrosoglutathione reductase from Chlamydomonas reinhardtii.
Authors: Tagliani, A. / Rossi, J. / Marchand, C.H. / De Mia, M. / Tedesco, D. / Gurrieri, L. / Meloni, M. / Falini, G. / Trost, P. / Lemaire, S.D. / Fermani, S. / Zaffagnini, M.
History
DepositionSep 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: S-(hydroxymethyl)glutathione dehydrogenase
B: S-(hydroxymethyl)glutathione dehydrogenase
C: S-(hydroxymethyl)glutathione dehydrogenase
D: S-(hydroxymethyl)glutathione dehydrogenase
E: S-(hydroxymethyl)glutathione dehydrogenase
F: S-(hydroxymethyl)glutathione dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,96833
Polymers242,7326
Non-polymers2,23527
Water40,5162249
1
A: S-(hydroxymethyl)glutathione dehydrogenase
F: S-(hydroxymethyl)glutathione dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,73912
Polymers80,9112
Non-polymers82810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-49 kcal/mol
Surface area28510 Å2
MethodPISA
2
B: S-(hydroxymethyl)glutathione dehydrogenase
C: S-(hydroxymethyl)glutathione dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,52610
Polymers80,9112
Non-polymers6158
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-64 kcal/mol
Surface area28920 Å2
MethodPISA
3
D: S-(hydroxymethyl)glutathione dehydrogenase
E: S-(hydroxymethyl)glutathione dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,70311
Polymers80,9112
Non-polymers7929
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-3 kcal/mol
Surface area29020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.832, 143.002, 206.174
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
S-(hydroxymethyl)glutathione dehydrogenase


Mass: 40455.410 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_12g543400v5 / Plasmid: pET3c / Production host: Escherichia coli (E. coli)
References: UniProt: A0A2K3D6R4, S-(hydroxymethyl)glutathione dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2249 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 0.1 M MgCl2 or Mg(CH3CO2)2, and 12-15% w/v PEG 20K or 12% w/v PEG 8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→56.973 Å / Num. obs: 208518 / % possible obs: 98.1 % / Redundancy: 5 % / Biso Wilson estimate: 13.624 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.035 / Rrim(I) all: 0.082 / Net I/σ(I): 13.9
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 9027 / CC1/2: 0.686 / Rpim(I) all: 0.373 / Rrim(I) all: 0.656

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DLA

4dla


Resolution: 1.8→56.973 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 21.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2045 20160 4.99 %Random selection
Rwork0.1733 384080 --
obs0.1749 208409 98.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.68 Å2 / Biso mean: 24.127 Å2 / Biso min: 8.63 Å2
Refinement stepCycle: final / Resolution: 1.8→56.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16926 0 105 2249 19280
Biso mean--31.48 31.33 -
Num. residues----2260
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.82050.32965310.31971130586
1.8205-1.84190.35236270.30221156088
1.8419-1.86430.3126880.28791187592
1.8643-1.88790.29176260.2721239094
1.8879-1.91280.26976250.25341250596
1.9128-1.9390.2767030.23771276098
1.939-1.96670.26116540.21761290299
1.9667-1.9960.23576640.20031305799
1.996-2.02720.22776830.192912952100
2.0272-2.06050.22296670.186113093100
2.0605-2.0960.22127100.182812949100
2.096-2.13410.2176790.181413028100
2.1341-2.17520.21557190.172412952100
2.1752-2.21960.22286810.179913004100
2.2196-2.26780.23586460.177413060100
2.2678-2.32060.23127110.176712975100
2.3206-2.37860.21126150.161813059100
2.3786-2.44290.20696040.160813076100
2.4429-2.51480.19916800.168113113100
2.5148-2.5960.22068350.173712849100
2.596-2.68880.22487200.173212963100
2.6888-2.79640.20236770.17212997100
2.7964-2.92370.20086600.167512965100
2.9237-3.07780.20056970.17331299499
3.0778-3.27060.19366740.16941297499
3.2706-3.52310.18526510.16181301299
3.5231-3.87760.18346930.15571298099
3.8776-4.43850.167210.14071287599
4.4385-5.59130.15526920.1391295499
5.5913-56.9730.16036270.14751290299

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