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- PDB-5tso: CRYSTAL STRUCTURE OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FRO... -

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Basic information

Entry
Database: PDB / ID: 5tso
TitleCRYSTAL STRUCTURE OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PIG MUSCLE COMPLEXED WITH ORTHOPHENANTHROLINE AT 1.90 ANGSTROM RESOLUTION
ComponentsGlyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD / NAD / GAPDH / GLYCOLYSIS / 1 / 10-ORTHOPHENANTHROLINE
Function / homology
Function and homology information


Glycolysis / peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / Gluconeogenesis / 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 ...Glycolysis / peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / Gluconeogenesis / 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 / GAIT complex / positive regulation of type I interferon production / defense response to fungus / lipid droplet / 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 / negative regulation of translation / protein stabilization / ribonucleoprotein complex / 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 / 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 / 1,10-PHENANTHROLINE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDimova, M. / Devedjiev, Y.D.
Citation
Journal: To Be Published
Title: Novel Enhancer Binding Site Found In Bacteria And Eukaryota But Not In Archea.
Authors: Dimova, M. / Devedjiev, Y.D.
#1: Journal: J Mol Biol. / Year: 1988
Title: Coenzyme-induced conformational changes in glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus
Authors: Skarzynski, T. / Wonacott, A.J.
History
DepositionOct 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Atomic model
Revision 1.2Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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
P: Glyceraldehyde-3-phosphate dehydrogenase
R: Glyceraldehyde-3-phosphate dehydrogenase
S: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,06128
Polymers107,6493
Non-polymers4,41225
Water15,907883
1
P: Glyceraldehyde-3-phosphate dehydrogenase
R: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

P: Glyceraldehyde-3-phosphate dehydrogenase
R: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,18836
Polymers143,5324
Non-polymers5,65632
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area14660 Å2
ΔGint-102 kcal/mol
Surface area45970 Å2
MethodPISA
2
S: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

S: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

S: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules

S: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,86940
Polymers143,5324
Non-polymers6,33736
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area14630 Å2
ΔGint-99 kcal/mol
Surface area45900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.480, 133.520, 210.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11S-815-

HOH

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Components

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Protein , 1 types, 3 molecules PRS

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


Mass: 35883.016 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: P00355, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups

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Non-polymers , 5 types, 908 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-PHN / 1,10-PHENANTHROLINE / 1,10-Phenanthroline


Mass: 180.205 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H8N2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 883 / 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: 3.03 Å3/Da / Density % sol: 59.38 % / Description: orthorhombic plates
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.005M 1,10-ORTHOPHENANTHROLINE, 0.05M HEPES, PH 8.0, 54.7%(W/V)AMMONIUM SULFATE,0.005 M EDTA, HANGING DROP, TEMPERATURE 277 K
PH range: 8

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 15, 2005
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR WITH SAGITTAL FOCUSSING
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→43.54 Å / Num. obs: 87846 / % possible obs: 93.6 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 12
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.159 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GD1

1gd1


Resolution: 1.9→43.54 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.095 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1319 1.5 %RANDOM
Rwork0.132 ---
obs0.133 87846 93.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7530 0 285 883 8698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197977
X-RAY DIFFRACTIONr_bond_other_d0.0020.027541
X-RAY DIFFRACTIONr_angle_refined_deg2.0191.98210827
X-RAY DIFFRACTIONr_angle_other_deg0.959317346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0165993
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.35724.519312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.811151281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4161530
X-RAY DIFFRACTIONr_chiral_restr0.1350.21228
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028912
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021799
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_it3.983.2153981
X-RAY DIFFRACTIONr_mcbond_other3.9793.2153980
X-RAY DIFFRACTIONr_mcangle_it4.2424.8034971
X-RAY DIFFRACTIONr_mcangle_other4.2414.8034972
X-RAY DIFFRACTIONr_scbond_it4.6343.6323992
X-RAY DIFFRACTIONr_scbond_other4.6343.6323992
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0435.2495851
X-RAY DIFFRACTIONr_long_range_B_refined5.28228.1059647
X-RAY DIFFRACTIONr_long_range_B_other5.12327.5299281
X-RAY DIFFRACTIONr_rigid_bond_restr7.026315514
X-RAY DIFFRACTIONr_sphericity_free21.8345306
X-RAY DIFFRACTIONr_sphericity_bonded9.266515973
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 65 -
Rwork0.297 4230 -
obs--61.71 %

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