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- PDB-1j0x: Crystal structure of the rabbit muscle glyceraldehyde-3-phosphate... -

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Basic information

Entry
Database: PDB / ID: 1j0x
TitleCrystal structure of the rabbit muscle glyceraldehyde-3-phosphate dehydrogenase (GAPDH)
Componentsglyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / Rossmann fold / mammalian GAPDH / apoptosis / negative cooperativity
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) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / GAIT complex / glycolytic process / microtubule cytoskeleton organization / glucose metabolic process / NAD binding ...Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / peptidyl-cysteine S-trans-nitrosylation / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / GAIT complex / glycolytic process / microtubule cytoskeleton organization / glucose metabolic process / NAD binding / microtubule cytoskeleton / regulation of translation / NADP binding / microtubule binding / neuron apoptotic process / protein stabilization / 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 speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCowan-Jacob, S.W. / Kaufmann, M. / Anselmo, A.N. / Stark, W. / Grutter, M.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of rabbit-muscle glyceraldehyde-3-phosphate dehydrogenase.
Authors: Cowan-Jacob, S.W. / Kaufmann, M. / Anselmo, A.N. / Stark, W. / Grutter, M.G.
History
DepositionNov 25, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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
Q: glyceraldehyde-3-phosphate dehydrogenase
R: glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,3506
Polymers143,0234
Non-polymers1,3272
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16980 Å2
ΔGint-112 kcal/mol
Surface area44570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.70, 98.50, 183.10
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsChain O, P, Q, R form the biologically active tetramer

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Components

#1: Protein
glyceraldehyde-3-phosphate dehydrogenase / Glyceraldehyde 3-phosphate dehydrogenase / GAPDH


Mass: 35755.766 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit)
References: UniProt: P46406, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.48 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: PEG 3350, HEPES, K3-citrate, microseeding, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
116 %(w/v)PEG33501reservoir
20.1 MHEPES1reservoirpH8.0
30.2 Mpotassium citrate1reservoir
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: Mirror
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.4→17.93 Å / Num. all: 58424 / Num. obs: 56521 / % possible obs: 96.6 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.034
Reflection shellResolution: 2.4→2.49 Å / % possible all: 86.1
Reflection
*PLUS
Redundancy: 3.4 % / Num. measured all: 194719 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 86.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.227

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Processing

Software
NameVersionClassification
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
TRUNCATEdata reduction
AMoREphasing
CNSrefinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Dimer of PDB ENTRY 1GD1

1gd1


Resolution: 2.4→17.93 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: torsion angle molecular dynamics simulated annealing maximum likelihood minimization individual B-factor refinement NCS-restraints. The structure was also refined with X-PLOR and CNX
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2853 -RANDOM
Rwork0.203 ---
all-58424 --
obs-56188 96.2 %-
Displacement parametersBiso mean: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1--9.17 Å20 Å20 Å2
2--0.15 Å20 Å2
3---9.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.4→17.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10044 0 88 473 10605
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.311 440 -
Rwork0.257 --
obs-7939 87.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2CSW.paramCSW.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4CSX.paramCSX.top
X-RAY DIFFRACTION5NAD.paramNAD.top

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