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- PDB-6lgj: Crystal structure of an oxido-reductase -

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Basic information

Entry
Database: PDB / ID: 6lgj
TitleCrystal structure of an oxido-reductase
ComponentsGlyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Inhibitor
Function / homology
Function and homology information


late endosome lumen / Glycolysis / Gluconeogenesis / peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glyceraldehyde-3-phosphate biosynthetic process ...late endosome lumen / Glycolysis / Gluconeogenesis / peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / negative regulation of vascular associated smooth muscle cell apoptotic process / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glyceraldehyde-3-phosphate biosynthetic process / GAIT complex / canonical glycolysis / positive regulation of type I interferon production / postsynaptic density, intracellular component / nitric oxide mediated signal transduction / cAMP-mediated signaling / gluconeogenesis / glycolytic process / microtubule cytoskeleton organization / NAD binding / microtubule cytoskeleton / myelin sheath / NADP binding / microtubule binding / neuron apoptotic process / positive regulation of canonical NF-kappaB signal transduction / negative regulation of translation / protein stabilization / innate immune response / glutamatergic synapse / enzyme binding / mitochondrion / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYang, Y. / Lei, J. / Yin, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: To be published
Title: Crystal structure of an oxido-reductase
Authors: Yang, Y. / Lei, J. / Yin, L.
History
DepositionDec 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: 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
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
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
C: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,0628
Polymers143,4084
Non-polymers2,6544
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19340 Å2
ΔGint-134 kcal/mol
Surface area43660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.140, 112.170, 84.830
Angle α, β, γ (deg.)90.000, 93.010, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 35851.957 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gapdh, Gapd / Production host: Escherichia coli (E. coli)
References: UniProt: P16858, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating), Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.51 Å3/Da / Density % sol: 51.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris, pH8.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→47.98 Å / Num. obs: 49776 / % possible obs: 95.66 % / Redundancy: 3.1 % / Biso Wilson estimate: 29.41 Å2 / CC1/2: 0.978 / Net I/σ(I): 5.18
Reflection shellResolution: 2.4→2.486 Å / Num. unique obs: 4985 / CC1/2: 0.927

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WNC

4wnc


Resolution: 2.4→47.979 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.74
RfactorNum. reflection% reflection
Rfree0.2159 1992 4 %
Rwork0.1587 --
obs0.161 49776 95.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89 Å2 / Biso mean: 29.4078 Å2 / Biso min: 9.52 Å2
Refinement stepCycle: final / Resolution: 2.4→47.979 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10056 0 176 450 10682
Biso mean--26.37 32 -
Num. residues----1332
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910436
X-RAY DIFFRACTIONf_angle_d1.02514164
X-RAY DIFFRACTIONf_chiral_restr0.0581612
X-RAY DIFFRACTIONf_plane_restr0.0061804
X-RAY DIFFRACTIONf_dihedral_angle_d15.2266204
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4001-2.46010.3121500.1996342296
2.4601-2.52660.2641410.1807341196
2.5266-2.60090.26521380.1799343197
2.6009-2.68490.24191460.1773345497
2.6849-2.78080.25351310.1756346297
2.7808-2.89210.24941460.1814343996
2.8921-3.02380.22761350.1791333994
3.0238-3.18310.26551580.1734339895
3.1831-3.38250.2331290.1648340795
3.3825-3.64360.19251410.1634330293
3.6436-4.01010.19191460.1412345096
4.0101-4.590.1541430.1229333094
4.59-5.78130.17971430.1353338394
5.7813-47.90.19191450.1492355697
Refinement TLS params.Method: refined / Origin x: 14.9176 Å / Origin y: 6.501 Å / Origin z: 20.7165 Å
111213212223313233
T0.1461 Å2-0.0027 Å2-0.0058 Å2-0.1197 Å20.005 Å2--0.1471 Å2
L0.4848 °2-0.0963 °2-0.0721 °2-0.4351 °2-0.1024 °2--0.721 °2
S-0.0112 Å °-0.0077 Å °0.0279 Å °0.0448 Å °0.0289 Å °0.0179 Å °-0.0322 Å °-0.0336 Å °-0.0164 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 335
2X-RAY DIFFRACTION1allA336
3X-RAY DIFFRACTION1allB3 - 335
4X-RAY DIFFRACTION1allB336
5X-RAY DIFFRACTION1allC3 - 335
6X-RAY DIFFRACTION1allC336
7X-RAY DIFFRACTION1allD3 - 335
8X-RAY DIFFRACTION1allD336
9X-RAY DIFFRACTION1allS1 - 471

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