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- PDB-6qun: Crystal structure of AtGapC1 with the catalytic Cys149 irreversib... -

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Basic information

Entry
Database: PDB / ID: 6qun
TitleCrystal structure of AtGapC1 with the catalytic Cys149 irreversibly oxidized by H2O2 treatment
ComponentsGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic
KeywordsOXIDOREDUCTASE / Rossman fold / NAD binding / Glycolytic process / oxidative stress / Hydrogen peroxide
Function / homology
Function and homology information


fruit development / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / salicylic acid binding / seed development / response to sucrose / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / plant-type vacuole / apoplast / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / mitochondrial envelope ...fruit development / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / salicylic acid binding / seed development / response to sucrose / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / plant-type vacuole / apoplast / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / mitochondrial envelope / response to redox state / chloroplast / gluconeogenesis / glycolytic process / response to hydrogen peroxide / NAD binding / NADP binding / response to heat / response to oxidative stress / copper ion binding / positive regulation of DNA-templated transcription / mitochondrion / DNA binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 ...Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFermani, S. / Zaffagnini, M. / Falini, G. / Trost, P.
Funding support Italy, 1items
OrganizationGrant numberCountry
FARB2012-University of Bologna Italy
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Glutathionylation primes soluble glyceraldehyde-3-phosphate dehydrogenase for late collapse into insoluble aggregates.
Authors: Zaffagnini, M. / Marchand, C.H. / Malferrari, M. / Murail, S. / Bonacchi, S. / Genovese, D. / Montalti, M. / Venturoli, G. / Falini, G. / Baaden, M. / Lemaire, S.D. / Fermani, S. / Trost, P.
History
DepositionFeb 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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

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Assembly

Deposited unit
O: Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic
R: Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,09911
Polymers73,0992
Non-polymers1,9999
Water59433
1
O: Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic
R: Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic
hetero molecules

O: Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic
R: Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,19722
Polymers146,1994
Non-polymers3,99918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_556x,x-y,-z+7/61
Buried area22310 Å2
ΔGint-318 kcal/mol
Surface area45810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.677, 77.677, 407.346
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11O-404-

SO4

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Components

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic / NAD-dependent glyceraldehydephosphate dehydrogenase C subunit 1


Mass: 36549.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The catalytic cysteine is oxidated to sulphinic acid
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GAPC1, GAPC, GAPDH, At3g04120, T6K12.26 / Production host: Escherichia coli (E. coli)
References: UniProt: P25858, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: 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
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3.0 M (NH4)2SO4, 0.1 M Hepes-NaOH (pH 7.5), 0.1 mM H2O2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.26 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 15, 2012
Details: Cilindrical Mirror with 50 nm Pt-coating, oridal Mirros with 50 nm Pt-coating
RadiationMonochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.26 Å / Relative weight: 1
ReflectionResolution: 3→47.79 Å / Num. obs: 15798 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 62.2 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.043 / Rrim(I) all: 0.12 / Net I/σ(I): 13.5
Reflection shellResolution: 3→3.16 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 2164 / Rpim(I) all: 0.168 / Rrim(I) all: 0.483 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z0H

4z0h


Resolution: 3→47.785 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / Phase error: 29.72
RfactorNum. reflection% reflectionSelection details
Rfree0.2918 1371 4.99 %random selection
Rwork0.2279 ---
obs0.231 15739 99.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 72.9 Å2
Refinement stepCycle: LAST / Resolution: 3→47.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5248 0 15 33 5296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045360
X-RAY DIFFRACTIONf_angle_d0.9327276
X-RAY DIFFRACTIONf_dihedral_angle_d6.1923186
X-RAY DIFFRACTIONf_chiral_restr0.057832
X-RAY DIFFRACTIONf_plane_restr0.007906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.10740.44811160.34112661X-RAY DIFFRACTION100
3.1074-3.23180.33771570.29432555X-RAY DIFFRACTION100
3.2318-3.37890.34221330.27292620X-RAY DIFFRACTION100
3.3789-3.55690.34561580.28312573X-RAY DIFFRACTION100
3.5569-3.77970.3151350.26422586X-RAY DIFFRACTION100
3.7797-4.07140.33041580.24372649X-RAY DIFFRACTION100
4.0714-4.48090.28371200.19872587X-RAY DIFFRACTION100
4.4809-5.12860.22331280.18072643X-RAY DIFFRACTION100
5.1286-6.4590.29081220.20352634X-RAY DIFFRACTION100
6.459-47.79120.21741440.18212597X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 38.4077 Å / Origin y: 37.11 Å / Origin z: 236.3742 Å
111213212223313233
T0.4902 Å2-0.0776 Å2-0.0111 Å2-0.6789 Å20.0345 Å2--0.3243 Å2
L0.768 °2-0.2203 °20.0211 °2-0.8754 °20.3847 °2--3.0027 °2
S0.0272 Å °0.1189 Å °0.176 Å °0.0492 Å °-0.1132 Å °0.1724 Å °-0.5829 Å °-0.5358 Å °0.1271 Å °
Refinement TLS groupSelection details: (chain O and resseq 0:337) or (chain R and resseq 0:337)

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