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- PDB-4z0h: X-ray structure of cytoplasmic glyceraldehyde-3-phosphate dehydro... -

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Basic information

Entry
Database: PDB / ID: 4z0h
TitleX-ray structure of cytoplasmic glyceraldehyde-3-phosphate dehydrogenase (GapC1) complexed with NAD
ComponentsGlyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic
KeywordsOXIDOREDUCTASE / Cytoplasm / glycolysis / Rossmann fold / NAD complex
Function / homology
Function and homology information


fruit development / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / seed development / salicylic acid binding / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / response to sucrose / apoplast / plant-type vacuole / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / mitochondrial envelope ...fruit development / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / seed development / salicylic acid binding / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / response to sucrose / apoplast / plant-type vacuole / 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 / molecular replacement / Resolution: 2.3 Å
AuthorsFermani, S. / Zaffagnini, M. / Orru, R. / Falini, G. / Trost, P.
Funding support Italy, 1items
OrganizationGrant numberCountry
University of BolognaFARB2012Francia Italy
CitationJournal: Antioxid. Redox Signal. / Year: 2016
Title: Tuning Cysteine Reactivity and Sulfenic Acid Stability by Protein Microenvironment in Glyceraldehyde-3-Phosphate Dehydrogenases of Arabidopsis thaliana.
Authors: Zaffagnini, M. / Fermani, S. / Calvaresi, M. / Orru, R. / Iommarini, L. / Sparla, F. / Falini, G. / Bottoni, A. / Trost, P.
History
DepositionMar 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Jan 10, 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
O: Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic
R: Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,03511
Polymers73,0352
Non-polymers1,9999
Water3,297183
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)150,06922
Polymers146,0714
Non-polymers3,99918
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_556x,x-y,-z+7/61
Buried area22930 Å2
ΔGint-364 kcal/mol
Surface area44030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.849, 76.849, 406.626
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11O-404-

SO4

21O-533-

HOH

31O-582-

HOH

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Components

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


Mass: 36517.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: GAPC1, GAPC, GAPDH, At3g04120, T6K12.26 / Plasmid: pET28a(+) / Details (production host): Novagen / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P25858, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical ChemComp-NAD / 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


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


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.37 Å3/Da / Density % sol: 48.17 % / Description: rombohedral
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 3.0-3.5 M ammonium sulphate, 0.1 M Na-Hepes. / PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 31, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.18→101.66 Å / Num. obs: 38786 / % possible obs: 99.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 8.4
Reflection shellResolution: 2.18→2.3 Å / Redundancy: 6 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 2.2 / % possible all: 98.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K2B

3k2b


Resolution: 2.3→67.77 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.915 / SU B: 10.592 / SU ML: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.44 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2777 1653 5 %RANDOM
Rwork0.2493 ---
obs0.2508 31304 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 102.59 Å2 / Biso mean: 47.534 Å2 / Biso min: 13.85 Å2
Baniso -1Baniso -2Baniso -3
1-3.46 Å21.73 Å20 Å2
2--3.46 Å20 Å2
3----5.19 Å2
Refinement stepCycle: final / Resolution: 2.3→67.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5127 0 123 183 5433
Biso mean--44.61 42.76 -
Num. residues----667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225347
X-RAY DIFFRACTIONr_angle_refined_deg1.941.9847259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8735665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.57324.381210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.59115918
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1051526
X-RAY DIFFRACTIONr_chiral_restr0.1180.2831
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213898
X-RAY DIFFRACTIONr_mcbond_it1.0881.53303
X-RAY DIFFRACTIONr_mcangle_it1.91425342
X-RAY DIFFRACTIONr_scbond_it2.432044
X-RAY DIFFRACTIONr_scangle_it3.7874.51917
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 115 -
Rwork0.374 2240 -
all-2355 -
obs--99.75 %

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