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

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Basic information

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


Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / peptidyl-cysteine S-trans-nitrosylation / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / killing by host of symbiont cells / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / negative regulation of endopeptidase activity / aspartic-type endopeptidase inhibitor activity / Gluconeogenesis / GAIT complex ...Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / peptidyl-cysteine S-trans-nitrosylation / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / killing by host of symbiont cells / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / negative regulation of endopeptidase 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 / neuron apoptotic process / positive regulation of canonical NF-kappaB signal transduction / nuclear membrane / 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: 2.621 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
B: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
F: Glyceraldehyde-3-phosphate dehydrogenase
G: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,5518
Polymers144,7174
Non-polymers1,8344
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SEC-MALLS confirms tetramers
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16260 Å2
ΔGint-94 kcal/mol
Surface area45020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.022, 111.299, 69.742
Angle α, β, γ (deg.)90, 98.33, 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: 36179.230 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.: 4 / Source method: obtained synthetically / Formula: C20H42O11 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 46.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Condition F9 of the MORPHEUS crystallisation screen, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.62→86.1 Å / Num. obs: 28210 / % possible obs: 71.3 % / Redundancy: 17.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.4 / Rrim(I) all: 0.41 / Net I/σ(I): 9
Reflection shellResolution: 2.62→2.89 Å / Redundancy: 17.3 % / Rmerge(I) obs: 2.47 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1409 / CC1/2: 0.464 / Rrim(I) all: 2.54 / % possible all: 14

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Processing

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

6ynd


Resolution: 2.621→86.1 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.888 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.368
Details: Automated non-crystallographic restraints were used throughout, 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 throughout, 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 plus or minus 0.005. External secondary structure restraints to PDB ID 6YND were used.
RfactorNum. reflection% reflectionSelection details
Rfree0.2154 1459 -RANDOM
Rwork0.176 ---
obs0.1781 28210 71.3 %-
Displacement parametersBiso mean: 45.17 Å2
Baniso -1Baniso -2Baniso -3
1-1.7249 Å20 Å2-1.1874 Å2
2--0.1549 Å20 Å2
3----1.8798 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.621→86.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10124 0 40 132 10296
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00810481HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0314282HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3592SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1775HARMONIC5
X-RAY DIFFRACTIONt_it10397HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1381SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact7472SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion17.93
LS refinement shellResolution: 2.621→2.78 Å
RfactorNum. reflection% reflection
Rfree0.359 20 -
Rwork0.2307 --
obs--8.82 %

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