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- PDB-4o59: Co-enzyme Induced Conformational Changes in Bovine Eye Glyceralde... -

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Basic information

Entry
Database: PDB / ID: 4o59
TitleCo-enzyme Induced Conformational Changes in Bovine Eye Glyceraldehyde 3-Phosphate Dehydrogenase
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
Keywordsoxidoreductase / transferase
Function / homology
Function and homology information


regulation of neurotransmitter loading into synaptic vesicle / Glycolysis / Gluconeogenesis / peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / extrinsic component of synaptic vesicle membrane / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / GAIT complex ...regulation of neurotransmitter loading into synaptic vesicle / Glycolysis / Gluconeogenesis / peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / extrinsic component of synaptic vesicle membrane / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / GAIT complex / positive regulation of type I interferon production / glycolytic process / microtubule cytoskeleton organization / glucose metabolic process / microtubule cytoskeleton / disordered domain specific binding / NAD binding / NADP binding / regulation of translation / microtubule binding / positive regulation of canonical NF-kappaB signal transduction / neuron apoptotic process / protein stabilization / innate immune response / nucleus / 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 Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsBaker, B.Y. / Shi, W. / Wang, B. / Palczewski, K.
CitationJournal: Protein Sci. / Year: 2014
Title: High-resolution crystal structures of the photoreceptor glyceraldehyde 3-phosphate dehydrogenase (GAPDH) with three and four-bound NAD molecules.
Authors: Baker, B.Y. / Shi, W. / Wang, B. / Palczewski, K.
History
DepositionDec 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: Glyceraldehyde-3-phosphate dehydrogenase
P: Glyceraldehyde-3-phosphate dehydrogenase
R: Glyceraldehyde-3-phosphate dehydrogenase
Q: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,7858
Polymers143,1314
Non-polymers2,6544
Water10,485582
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19420 Å2
ΔGint-134 kcal/mol
Surface area44190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.703, 125.273, 83.602
Angle α, β, γ (deg.)90.00, 118.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 35782.848 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Rod Outer Segment / Source: (natural) Bos taurus (cattle) / Tissue: Retinas
References: UniProt: P10096, 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.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 582 / 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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 20% PEG3350, 0.15 M malic acid pH 7.0, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. obs: 220468 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.094

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Processing

Software
NameVersionClassification
Xtaldata collection
PHASERphasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J0X

1j0x


Resolution: 1.52→47.8 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.455 / SU ML: 0.053 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.072 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20904 10886 5 %RANDOM
Rwork0.17822 ---
obs0.17977 206213 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.959 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20.58 Å2
2---0.22 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.52→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10052 0 176 582 10810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.01910444
X-RAY DIFFRACTIONr_bond_other_d0.0010.029992
X-RAY DIFFRACTIONr_angle_refined_deg2.0621.96614176
X-RAY DIFFRACTIONr_angle_other_deg0.924322996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69651324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.95624.615416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.315151724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0881540
X-RAY DIFFRACTIONr_chiral_restr0.1270.21612
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211808
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022348
X-RAY DIFFRACTIONr_mcbond_it1.6041.5785308
X-RAY DIFFRACTIONr_mcbond_other1.5961.5775307
X-RAY DIFFRACTIONr_mcangle_it2.1852.3676628
X-RAY DIFFRACTIONr_mcangle_other2.1872.3676629
X-RAY DIFFRACTIONr_scbond_it2.8371.8615136
X-RAY DIFFRACTIONr_scbond_other2.8371.8615137
X-RAY DIFFRACTIONr_scangle_other4.2412.657549
X-RAY DIFFRACTIONr_long_range_B_refined5.03413.08711777
X-RAY DIFFRACTIONr_long_range_B_other5.01612.96411593
LS refinement shellResolution: 1.522→1.562 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 763 -
Rwork0.302 14502 -
all-15265 -
obs--93.74 %

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