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- PDB-4gl4: Crystal structure of oxidized S-nitrosoglutathione reductase from... -

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Basic information

Entry
Database: PDB / ID: 4gl4
TitleCrystal structure of oxidized S-nitrosoglutathione reductase from Arabidopsis thalina, complex with NADH
ComponentsAlcohol dehydrogenase class-3
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / reduction of GSNO / NADH binding
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 / 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. / 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
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Alcohol dehydrogenase class-3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsWeichsel, A. / Crotty, J. / Montfort, W.R.
CitationJournal: To be Published
Title: Crystal structure and kinetic behavior of alcohol dehydrogenase III/S-nitrosoglutathione reductase from arabidopsis thalina
Authors: Crotty, J. / Greving, M. / Brettschneider, S. / Weichsel, A. / Wildner, G.F. / Vierling, E. / Montfort, W.R.
History
DepositionAug 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Non-polymer description
Revision 1.2Sep 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_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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,97620
Polymers81,2312
Non-polymers2,74518
Water6,684371
1
A: Alcohol dehydrogenase class-3
hetero molecules

A: Alcohol dehydrogenase class-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,16822
Polymers81,2312
Non-polymers2,93720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
2
B: Alcohol dehydrogenase class-3
hetero molecules

B: Alcohol dehydrogenase class-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,78418
Polymers81,2312
Non-polymers2,55316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-19 kcal/mol
Surface area29020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.634, 91.634, 173.184
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-563-

HOH

21A-649-

HOH

31B-534-

HOH

41B-652-

HOH

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Components

#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: 40615.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ADH2, ADHIII, FDH1, At5g43940, MRH10.4 / Plasmid: pJC20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q96533, alcohol dehydrogenase, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor, S-(hydroxymethyl)glutathione dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.1 M ammonium sulfate, 100 mM Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 18, 2006 / Details: bent Si-mirror
RadiationMonochromator: diamond (111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→27.2 Å / Num. all: 93100 / Num. obs: 93100 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 10.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 10 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.2 / Num. unique all: 9201 / % possible all: 100

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Processing

Software
NameClassification
Blu-Icedata collection
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3UKO

3uko


Resolution: 1.8→27.13 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.359 / SU ML: 0.099 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23604 3957 5 %RANDOM
Rwork0.19635 ---
all0.19834 74638 --
obs0.19834 74638 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.242 Å
Refinement stepCycle: LAST / Resolution: 1.8→27.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5690 0 152 371 6213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.026181
X-RAY DIFFRACTIONr_bond_other_d0.0010.024072
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.9948459
X-RAY DIFFRACTIONr_angle_other_deg0.9853.00110045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6595809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03524.783230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45151027
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3671522
X-RAY DIFFRACTIONr_chiral_restr0.0960.2977
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021199
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 296 -
Rwork0.373 5074 -
obs-5074 100 %

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