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- PDB-7aau: Crystal structure of nitrosoglutathione reductase from Chlamydomo... -

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Basic information

Entry
Database: PDB / ID: 7aau
TitleCrystal structure of nitrosoglutathione reductase 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 (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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / S-(hydroxymethyl)glutathione dehydrogenase
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsFermani, S. / Zaffagnini, M. / Falini, G. / Lemaire, S.D.
Funding support Italy, France, 2items
OrganizationGrant numberCountry
Other governmentAlma Idea 2017 Program 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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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)249,25644
Polymers242,7326
Non-polymers6,52338
Water26,1761453
1
A: S-(hydroxymethyl)glutathione dehydrogenase
F: S-(hydroxymethyl)glutathione dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,23117
Polymers80,9112
Non-polymers2,32015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-94 kcal/mol
Surface area27320 Å2
MethodPISA
2
B: S-(hydroxymethyl)glutathione dehydrogenase
C: S-(hydroxymethyl)glutathione dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,99514
Polymers80,9112
Non-polymers2,08412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-72 kcal/mol
Surface area27930 Å2
MethodPISA
3
D: S-(hydroxymethyl)glutathione dehydrogenase
E: S-(hydroxymethyl)glutathione dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,03013
Polymers80,9112
Non-polymers2,11911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-24 kcal/mol
Surface area27570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.754, 142.723, 206.587
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#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

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Non-polymers , 6 types, 1491 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 106.120 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1453 / 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: 2.4 Å3/Da / Density % sol: 48 % / Description: stick crystals
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: ELETTRA / Beamline: 5.2R / Wavelength: 0.9137 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9137 Å / Relative weight: 1
ReflectionResolution: 2.3→117.4 Å / Num. obs: 102418 / % possible obs: 99.7 % / Redundancy: 4.2 % / Biso Wilson estimate: 22.16 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.087 / Rrim(I) all: 0.18 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.3-2.343.90.7962.248610.6550.460.92396.9
12.6-117.43.80.05319.37120.9960.0310.06296.8

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DLA

4dla


Resolution: 2.301→48.565 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.13 / Phase error: 23.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 9672 4.92 %Random selection
Rwork0.1781 186814 --
obs0.1805 102297 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.48 Å2 / Biso mean: 31.6457 Å2 / Biso min: 12.89 Å2
Refinement stepCycle: final / Resolution: 2.301→48.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16948 0 382 1453 18783
Biso mean--31.99 35.16 -
Num. residues----2263
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.301-2.32680.33933300.2808595995
2.3268-2.35420.30793300.25136238100
2.3542-2.38290.29262920.23576212100
2.3829-2.4130.30623410.24046218100
2.413-2.44480.2813040.23586240100
2.4448-2.47830.29742950.23996280100
2.4783-2.51370.3143260.23736295100
2.5137-2.55120.29913410.22816187100
2.5512-2.59110.29012940.23186300100
2.5911-2.63350.33163430.23496187100
2.6335-2.67890.28293200.22916268100
2.6789-2.72770.26393090.22176226100
2.7277-2.78010.27813550.20886215100
2.7801-2.83690.2453250.19866231100
2.8369-2.89850.24843340.1956281100
2.8985-2.96590.25323310.20236176100
2.9659-3.04010.26833010.20276270100
3.0401-3.12230.25133140.19796264100
3.1223-3.21420.25383840.19486172100
3.2142-3.31790.23423330.18256216100
3.3179-3.43640.20533480.17266224100
3.4364-3.5740.22012850.16256278100
3.574-3.73660.17663060.15256261100
3.7366-3.93350.20623330.15016230100
3.9335-4.17980.17483050.13966255100
4.1798-4.50230.17442950.12446279100
4.5023-4.9550.14772920.12326235100
4.955-5.67110.18713190.14416229100
5.6711-7.14130.18133410.15746236100
7.1413-48.5650.16273460.1446615299

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