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- PDB-4dl9: Crystal structure of S-nitrosoglutathione reductase from tomato (... -

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Basic information

Entry
Database: PDB / ID: 4dl9
TitleCrystal structure of S-nitrosoglutathione reductase from tomato (Solanum lycopersicum) in complex with NAD+
ComponentsAlcohol dehydrogenase class III
KeywordsOXIDOREDUCTASE / Rossmann fold / alcohol dehydrogenase class-3 / S-nitrosoglutathione / NAD+
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. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily ...Alcohol dehydrogenase class III / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / S-(hydroxymethyl)glutathione dehydrogenase
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKopecny, D. / Tylichova, M. / Briozzo, P.
CitationJournal: Biochimie / Year: 2013
Title: Structural and functional characterization of a plant S-nitrosoglutathione reductase from Solanum lycopersicum.
Authors: Kubienova, L. / Kopecny, D. / Tylichova, M. / Briozzo, P. / Skopalova, J. / Sebela, M. / Navratil, M. / Tache, R. / Luhova, L. / Barroso, J.B. / Petrivalsky, M.
History
DepositionFeb 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Mar 20, 2013Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alcohol dehydrogenase class III
B: Alcohol dehydrogenase class III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,33012
Polymers85,1672
Non-polymers2,16310
Water11,205622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-35 kcal/mol
Surface area28650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.114, 125.076, 76.761
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-791-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alcohol dehydrogenase class III


Mass: 42583.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum lycopersicum (tomato) / Strain: cv. Amateur / Gene: ADH3, GSNOR / Plasmid: pCDFDuet / Production host: Escherichia coli (E. coli) / Strain (production host): T7 express / References: UniProt: D2Y3F4, alcohol dehydrogenase

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Non-polymers , 5 types, 632 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 622 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES pH 6.5, 14% PEG 20000, 4% glycerol (plus 2.5 mM NAD+ in the drop), VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.85→25 Å / Num. all: 68610 / Num. obs: 68193 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 24.85 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.05
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.85-1.960.5672.2110934197.7
1.96-2.090.3544.0210299199.7
2.09-2.260.2275.869623199.8
2.26-2.470.1518.218873199.9
2.47-2.770.10211.348039199.9
2.77-3.190.05817.557154199.8
3.19-3.90.03626.656078199.8
3.9-5.50.02932.774795199.6
5.5-250.02633.972815197.8

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TEH

1teh


Resolution: 1.85→24.88 Å / Cor.coef. Fo:Fc: 0.9345 / Cor.coef. Fo:Fc free: 0.9164 / SU R Cruickshank DPI: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 3437 5.07 %RANDOM
Rwork0.1805 ---
all0.1825 68610 --
obs0.1825 67833 99.57 %-
Displacement parametersBiso mean: 30.5 Å2
Baniso -1Baniso -2Baniso -3
1--15.3034 Å20 Å20 Å2
2--9.6552 Å20 Å2
3---5.6482 Å2
Refine analyzeLuzzati coordinate error obs: 0.222 Å
Refinement stepCycle: LAST / Resolution: 1.85→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5698 0 128 622 6448
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015969HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.098114HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2055SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes133HARMONIC2
X-RAY DIFFRACTIONt_gen_planes911HARMONIC5
X-RAY DIFFRACTIONt_it5969HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.57
X-RAY DIFFRACTIONt_other_torsion16.7
X-RAY DIFFRACTIONt_chiral_improper_torsion786SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7619SEMIHARMONIC4
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2975 231 4.77 %
Rwork0.2407 4607 -
all0.2434 4838 -
obs--99.57 %

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