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- PDB-6ade: Crystal structure of phosphorylated mutant of glyceraldehyde 3-ph... -

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Basic information

Entry
Database: PDB / ID: 6ade
TitleCrystal structure of phosphorylated mutant of glyceraldehyde 3-phosphate dehydrogenase from human placenta at 3.15A resolution
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / negative regulation of endopeptidase activity / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / killing by host of symbiont cells / aspartic-type endopeptidase inhibitor activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / Glycolysis / GAIT complex ...peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / negative regulation of endopeptidase activity / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / killing by host of symbiont cells / aspartic-type endopeptidase inhibitor activity / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / Gluconeogenesis / Glycolysis / GAIT complex / peptidyl-cysteine S-nitrosylase activity / positive regulation of type I interferon production / regulation of macroautophagy / defense response to fungus / lipid droplet / positive regulation of cytokine production / glycolytic process / cellular response to type II interferon / microtubule cytoskeleton organization / glucose metabolic process / antimicrobial humoral immune response mediated by antimicrobial peptide / NAD binding / disordered domain specific binding / NADP binding / microtubule cytoskeleton / microtubule binding / neuron apoptotic process / nuclear membrane / killing of cells of another organism / vesicle / positive regulation of canonical NF-kappaB signal transduction / negative regulation of translation / protein stabilization / ribonucleoprotein complex / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / extracellular exosome / identical protein binding / nucleus / membrane / 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 / 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 domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsDilawari, R. / Singh, P.K. / Raje, M. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal structure of phosphorylated mutant of glyceraldehyde 3-phosphate dehydrogenase from human placenta at 3.15A resolution
Authors: Dilawari, R. / Singh, P.K. / Raje, M. / Sharma, S. / Singh, T.P.
History
DepositionJul 31, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,3934
Polymers108,7293
Non-polymers6631
Water81145
1
A: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

A: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8134
Polymers72,4862
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area5520 Å2
ΔGint-48 kcal/mol
Surface area25790 Å2
MethodPISA
2
B: Glyceraldehyde-3-phosphate dehydrogenase

C: Glyceraldehyde-3-phosphate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)72,4862
Polymers72,4862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455-x-1/2,y+1/2,-z+1/21
Buried area2930 Å2
ΔGint-23 kcal/mol
Surface area26940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.780, 131.680, 220.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 3 - 335 / Label seq-ID: 3 - 335

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13BB
23CC

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 36243.102 Da / Num. of mol.: 3 / Mutation: K271L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GAPDH, GAPD, CDABP0047, OK/SW-cl.12 / Production host: Escherichia coli (E. coli)
References: UniProt: P04406, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.93 Å3/Da / Density % sol: 58.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.7 / Details: 4M sodium formate, pH 7.7 / PH range: 5-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.953 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 14, 2018 / Details: mirror
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 3.15→45.39 Å / Num. obs: 23302 / % possible obs: 100 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 5.6
Reflection shellResolution: 3.15→3.23 Å / Redundancy: 5 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1576 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U8F

1u8f


Resolution: 3.15→45.39 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.904 / SU B: 26.733 / SU ML: 0.413 / Cross valid method: THROUGHOUT / ESU R Free: 0.452 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23937 1161 5 %RANDOM
Rwork0.19398 ---
obs0.19627 22126 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 70 Å2
Baniso -1Baniso -2Baniso -3
1-4.16 Å2-0 Å20 Å2
2---5.61 Å2-0 Å2
3---1.46 Å2
Refinement stepCycle: 1 / Resolution: 3.15→45.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7590 0 44 45 7679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0147788
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177129
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.66410564
X-RAY DIFFRACTIONr_angle_other_deg0.841.65216645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1715996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6623.391345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.581151293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5241530
X-RAY DIFFRACTIONr_chiral_restr0.0560.21040
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028745
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021436
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.3927.2623993
X-RAY DIFFRACTIONr_mcbond_other5.3927.2613992
X-RAY DIFFRACTIONr_mcangle_it8.54110.8954986
X-RAY DIFFRACTIONr_mcangle_other8.5410.8974987
X-RAY DIFFRACTIONr_scbond_it5.9037.6993795
X-RAY DIFFRACTIONr_scbond_other5.9027.6993796
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.5111.3445579
X-RAY DIFFRACTIONr_long_range_B_refined15.55231758
X-RAY DIFFRACTIONr_long_range_B_other15.55231759
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A103280.07
12B103280.07
21A103430.08
22C103430.08
31B103110.07
32C103110.07
LS refinement shellResolution: 3.15→3.231 Å
RfactorNum. reflection% reflection
Rfree0.349 97 -
Rwork0.349 1576 -
obs--99.88 %

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