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- PDB-6yne: GAPDH purified from the supernatant of HEK293F cells: crystal for... -

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Basic information

Entry
Database: PDB / ID: 6yne
TitleGAPDH purified from the supernatant of HEK293F cells: crystal form 2 of 4.
ComponentsGlyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
KeywordsBIOSYNTHETIC PROTEIN / HEK293F / kifunensine
Function / homology
Function and homology information


peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / killing by host of symbiont cells / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / negative regulation of endopeptidase activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / aspartic-type endopeptidase inhibitor activity / Gluconeogenesis / GAIT complex ...peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / killing by host of symbiont cells / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / negative regulation of endopeptidase activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / aspartic-type endopeptidase inhibitor activity / Gluconeogenesis / GAIT complex / Glycolysis / positive regulation of type I interferon production / regulation of macroautophagy / defense response to fungus / lipid droplet / positive regulation of cytokine production / glycolytic process / microtubule cytoskeleton organization / cellular response to type II interferon / glucose metabolic process / NAD binding / microtubule cytoskeleton / disordered domain specific binding / antimicrobial humoral immune response mediated by antimicrobial peptide / NADP binding / microtubule binding / nuclear membrane / neuron apoptotic process / positive regulation of canonical NF-kappaB signal transduction / killing of cells of another organism / vesicle / negative regulation of translation / protein stabilization / ribonucleoprotein complex / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / extracellular exosome / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
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 / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.853 Å
AuthorsRoversi, P. / Lia, A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust204801/Z/16/Z United Kingdom
Wellcome Trust214090/Z/18/Z United Kingdom
CitationJournal: Wellcome Open Res / Year: 2020
Title: Partial catalytic Cys oxidation of human GAPDH to Cys-sulfonic acid.
Authors: Lia, A. / Dowle, A. / Taylor, C. / Santino, A. / Roversi, P.
History
DepositionApr 13, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _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
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
C: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,35817
Polymers144,3974
Non-polymers5,96113
Water10,251569
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALLS confirms tetramers
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20500 Å2
ΔGint-102 kcal/mol
Surface area45000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.787, 124.652, 79.74
Angle α, β, γ (deg.)90, 117.04, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase / Glyceraldehyde 3-phosphate dehydrogenase / GAPDH / Peptidyl-cysteine S-nitrosylase GAPDH


Mass: 36099.168 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / Organ: Kidney / Tissue: Epithelium
References: UniProt: P04406, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups
#2: Chemical
ChemComp-XPE / 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL / DECAETHYLENE GLYCOL / Polyethylene glycol


Mass: 458.541 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C20H42O11 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 569 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.51 Å3/Da / Density % sol: 50.94 % / Description: Prism
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MORPHEUS condition F9: 0.12M MORPHEUS monosaccharides solution , 0.1M MORPHEUS Buffer System 3, 30% v/v MORPHEUS Precipitant Mix 1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97622 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 22, 2019
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.85→72.85 Å / Num. obs: 81465 / % possible obs: 67.6 % / Redundancy: 7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.226 / Rrim(I) all: 0.245 / Net I/σ(I): 6.5
Reflection shellResolution: 1.85→2.05 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.488 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4074 / CC1/2: 0.456 / Rrim(I) all: 1.618 / % possible all: 12.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YND

6ynd


Resolution: 1.853→72.85 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.923 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.213 / SU Rfree Blow DPI: 0.157
Details: Automated non-crystallographic restraints were used throughtout, including water molecules (assigned to each chain using CCP4-Sortwater). At each catalytic Cys152 site, a 0.5:0.5 occupancy ...Details: Automated non-crystallographic restraints were used throughtout, including water molecules (assigned to each chain using CCP4-Sortwater). At each catalytic Cys152 site, a 0.5:0.5 occupancy ratio mixture of Cys and Cys S-Sulfonic acid was initially modelled in Fo-Fc residual density. At each Cys152 site, occupancies for Cys and Cys S-Sulfonic acid were refined and constrained so that they sum up to 1.000. External secondary structure restraints to PDB ID 6YND.
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 4059 -RANDOM
Rwork0.1903 ---
obs0.1911 81457 67.6 %-
Displacement parametersBiso mean: 30.35 Å2
Baniso -1Baniso -2Baniso -3
1-1.1261 Å20 Å20.5176 Å2
2--0.4886 Å20 Å2
3----1.6147 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.853→72.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10108 0 173 569 10850
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00820928HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0537896HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6308SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes3340HARMONIC5
X-RAY DIFFRACTIONt_it10529HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1388SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact16210SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.71
X-RAY DIFFRACTIONt_other_torsion15.61
LS refinement shellResolution: 1.853→1.98 Å
RfactorNum. reflection% reflection
Rfree0.2198 94 -
Rwork0.2182 --
obs--7.29 %

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