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- PDB-1u8f: Crystal Structure Of Human Placental Glyceraldehyde-3-Phosphate D... -

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Basic information

Entry
Database: PDB / ID: 1u8f
TitleCrystal Structure Of Human Placental Glyceraldehyde-3-Phosphate Dehydrogenase At 1.75 Resolution
ComponentsGlyceraldehyde-3-phosphate dehydrogenase, liverGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / GAPDH / ROSSMANN FOLD / DEHYDROGENASE / MAMMALIAN GAPDH / GAPD
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 / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsJenkins, J.L. / Tanner, J.J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2006
Title: High-resolution structure of human D-glyceraldehyde-3-phosphate dehydrogenase.
Authors: Jenkins, J.L. / Tanner, J.J.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: A human nuclear uracil DNA glycosylase is the 37-kDa subunit of glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Meyer-Siegler, K. / Mauro, D.J. / Seal, G. / Wurzer, J. / deRiel, J.K. / Sirover, M.A.
History
DepositionAug 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)146,3877
Polymers144,3974
Non-polymers1,9903
Water16,412911
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18500 Å2
ΔGint-118 kcal/mol
Surface area44440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.953, 125.651, 132.329
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glyceraldehyde-3-phosphate dehydrogenase, liver / Glyceraldehyde 3-phosphate dehydrogenase / GAPDH


Mass: 36099.168 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: PlacentalPlacentalia / Gene: GAPD / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P04406, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 911 / 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: 2.25 Å3/Da / Density % sol: 44.84 %
Crystal growTemperature: 295 K / pH: 7
Details: PEG 3350, SUCCINIC ACID, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 141888 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 23.1
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 4.1 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNPUBLISHED STRUCTURE

Resolution: 1.75→50 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3099319.22 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.217 14147 10 %RANDOM
Rwork0.191 ---
obs0.191 141888 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.28 Å2 / ksol: 0.44 e/Å3
Displacement parametersBiso mean: 16.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20 Å2
2--2 Å20 Å2
3----0.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10133 0 132 911 11176
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.11.5
X-RAY DIFFRACTIONc_mcangle_it1.642
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.772.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 2294 10 %
Rwork0.222 20638 -
obs--97.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5PARAM.NAD2.CNS

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