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

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Basic information

Entry
Database: PDB / ID: 6ynd
TitleGAPDH purified from the supernatant of HEK293F cells: crystal form 1 of 4.
ComponentsGlyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
KeywordsBIOSYNTHETIC PROTEIN / HEK293F / kifunensine / Cysteine-S-Sulfonic acid
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: 1.525 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
E: Glyceraldehyde-3-phosphate dehydrogenase
F: Glyceraldehyde-3-phosphate dehydrogenase
G: Glyceraldehyde-3-phosphate dehydrogenase
H: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,39521
Polymers289,4348
Non-polymers5,96113
Water29,5271639
1
A: Glyceraldehyde-3-phosphate dehydrogenase
C: Glyceraldehyde-3-phosphate dehydrogenase
E: Glyceraldehyde-3-phosphate dehydrogenase
H: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,0109
Polymers144,7174
Non-polymers2,2935
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16620 Å2
ΔGint-97 kcal/mol
Surface area46280 Å2
MethodPISA
2
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)148,38512
Polymers144,7174
Non-polymers3,6688
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17090 Å2
ΔGint-95 kcal/mol
Surface area46570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.885, 124.455, 141.986
Angle α, β, γ (deg.)90.00, 99.39, 90.00
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.: 8 / Mutation: C152X / Source method: isolated from a natural source
Details: GAPDH with catalytic Cys partially oxidised to Cys-S-Sulfonic Acid
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.: 1639 / 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: 2.48 Å3/Da / Density % sol: 50.34 % / Description: Prism
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M MORPHEUS Amino acids solution (DL-Glutamic acid; DL-Alanine; Glycine; DL-Lysine; DL-Serine), 0.1M MORPHEUS Buffer System 3 (Tris (base); BICINE), 30% v/v MORPHEUS Precipitant Mix 1 (40% ...Details: 0.1M MORPHEUS Amino acids solution (DL-Glutamic acid; DL-Alanine; Glycine; DL-Lysine; DL-Serine), 0.1M MORPHEUS Buffer System 3 (Tris (base); BICINE), 30% v/v MORPHEUS Precipitant Mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000)

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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 monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.52→140.09 Å / Num. obs: 295271 / % possible obs: 69.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 23.93 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.03 / Rrim(I) all: 0.09 / Net I/σ(I): 11.7
Reflection shellResolution: 1.52→1.71 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.071 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 14763 / CC1/2: 0.608 / Rpim(I) all: 0.444 / Rrim(I) all: 1.161 / % possible all: 12.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (19-MAR-2020)refinement
PROCORdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U8F

1u8f


Resolution: 1.525→140.09 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.104 / SU Rfree Blow DPI: 0.095 / SU Rfree Cruickshank DPI: 0.095
Details: Initial automated water addition and positional and individual B-factor refinement were carried out in autoBUSTER. Automated non-crystallographic restraints were used throughtout, including ...Details: Initial automated water addition and positional and individual B-factor refinement were carried out in autoBUSTER. 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 plus or minus 0.005.
RfactorNum. reflection% reflectionSelection details
Rfree0.1995 14686 4.97 %RANDOM
Rwork0.182 ---
obs0.1829 295271 69.4 %-
Displacement parametersBiso mean: 27.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.1084 Å20 Å2-0.0028 Å2
2--0.1391 Å20 Å2
3----0.0306 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.525→140.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20156 0 272 1639 22067
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00842354HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0276777HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d12877SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes6906HARMONIC5
X-RAY DIFFRACTIONt_it21324HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.79
X-RAY DIFFRACTIONt_other_torsion15.34
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2827SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies8HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact33311SEMIHARMONIC4
LS refinement shellResolution: 1.525→1.63 Å
RfactorNum. reflection% reflection
Rfree0.2256 332 5.62 %
Rwork0.2091 5574 -
obs--7.56 %

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