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- PDB-7av7: Crystal structure of S-nitrosylated nitrosoglutathione reductase(... -

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Basic information

Entry
Database: PDB / ID: 7av7
TitleCrystal structure of S-nitrosylated nitrosoglutathione reductase(GSNOR)from Chlamydomonas reinhardtii, in complex with NAD+
ComponentsS-(hydroxymethyl)glutathione dehydrogenase
KeywordsOXIDOREDUCTASE / Alcohol dehydrogenase / Zinc-binding dehydrogenase
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 / : / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / S-(hydroxymethyl)glutathione dehydrogenase
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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
DepositionNov 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)247,70725
Polymers242,9066
Non-polymers4,80119
Water86548
1
A: S-(hydroxymethyl)glutathione dehydrogenase
F: S-(hydroxymethyl)glutathione dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5578
Polymers80,9692
Non-polymers1,5886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-75 kcal/mol
Surface area27850 Å2
MethodPISA
2
B: S-(hydroxymethyl)glutathione dehydrogenase
C: S-(hydroxymethyl)glutathione dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5578
Polymers80,9692
Non-polymers1,5886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-45 kcal/mol
Surface area28300 Å2
MethodPISA
3
D: S-(hydroxymethyl)glutathione dehydrogenase
E: S-(hydroxymethyl)glutathione dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5939
Polymers80,9692
Non-polymers1,6247
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-50 kcal/mol
Surface area27710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.386, 143.294, 206.271
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: 40484.410 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_12g543400v5 / Plasmid: pET-3c / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9137 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 4, 2015 / Details: Cilindrical Mirror with 50 nm Pt-coating
RadiationMonochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9137 Å / Relative weight: 1
ReflectionResolution: 2.9→48.623 Å / Num. obs: 195324 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 30.7 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.081 / Rrim(I) all: 0.16 / Rsym value: 0.118 / Net I/av σ(I): 3.2 / Net I/σ(I): 8.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym value% possible all
2.9-3.063.50.5362.174440.7330.360.6930.53699
3.06-3.243.80.3052.471370.2030.4050.30599.8
3.24-3.4740.1923.867010.1260.2540.19299.8
3.47-3.743.90.1414.962790.0940.1890.14199.8
3.74-4.13.80.1056.857920.0720.1420.10599.9
4.1-4.593.50.0729.852470.0520.0980.07299.8
4.59-5.293.90.06311.346810.0420.0840.063100
5.29-6.483.80.0739.839850.050.0990.073100
6.48-9.173.50.0611.331290.0430.0810.0699.9
9.17-48.6233.70.055218360.0410.0740.05599.3

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AAU

7aau


Resolution: 2.9→48.5282 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 25.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2568 4863 4.91 %Random selection
Rwork0.18 94246 --
obs0.1837 52134 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.9 Å2 / Biso mean: 37.0267 Å2 / Biso min: 7.45 Å2
Refinement stepCycle: final / Resolution: 2.9→48.5282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16928 0 277 48 17253
Biso mean--50.72 21.11 -
Num. residues----2259
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9001-2.9330.32551810.261295296
2.933-2.96750.34291320.2613195100
2.9675-3.00370.36471660.26753139100
3.0037-3.04170.37851360.25913199100
3.0417-3.08170.34651710.24223120100
3.0817-3.12390.32381700.23893176100
3.1239-3.16860.28791590.22723134100
3.1686-3.21580.30851240.22243169100
3.2158-3.26610.30111790.2253185100
3.2661-3.31960.33271740.22123081100
3.3196-3.37680.32321790.21833110100
3.3768-3.43820.32481700.23423157100
3.4382-3.50430.30381770.2143118100
3.5043-3.57590.28851530.19863185100
3.5759-3.65360.2481390.1863156100
3.6536-3.73850.30511840.18573130100
3.7385-3.8320.26991630.1783104100
3.832-3.93560.28371520.17033221100
3.9356-4.05130.25881570.1683116100
4.0513-4.1820.21961570.15473166100
4.182-4.33140.24411220.15273182100
4.3314-4.50470.21351590.13143133100
4.5047-4.70960.17831900.12773148100
4.7096-4.95760.19941450.13183168100
4.9576-5.26790.20881860.13893131100
5.2679-5.67410.21481450.14833144100
5.6741-6.2440.22071800.14563145100
6.244-7.14510.21921910.14633142100
7.1451-8.99260.17151640.14353117100
8.9926-48.52820.20011580.1777312399

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